App-Anchr
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doc/model_organisms.md  view on Meta::CPAN 

| Q35L60X40P001  | 486.28M |   40.0 | 11870 | 11.33M | 1722 |     12095 | 11.12M | 1438 |       777 | 217.61K |  284 | "31,41,51,61,71,81" | 0:05'24'' | 0:01'25'' |
| Q35L60X40P002  | 486.28M |   40.0 | 11706 | 11.43M | 1712 |     11825 | 11.09M | 1431 |       975 |  335.6K |  281 | "31,41,51,61,71,81" | 0:07'22'' | 0:01'18'' |
| Q35L60X40P003  | 486.28M |   40.0 | 11991 | 11.36M | 1667 |     12276 | 11.16M | 1414 |       786 | 192.34K |  253 | "31,41,51,61,71,81" | 0:07'32'' | 0:01'16'' |
| Q35L60X80P000  | 972.57M |   80.0 |  9921 | 11.42M | 2046 |     10046 | 11.11M | 1683 |       816 |  311.6K |  363 | "31,41,51,61,71,81" | 0:10'27'' | 0:01'23'' |
| Q35L60X80P001  | 972.57M |   80.0 |  9705 | 11.43M | 2013 |      9937 | 11.13M | 1652 |       822 | 299.37K |  361 | "31,41,51,61,71,81" | 0:10'18'' | 0:01'41'' |
| Q35L60X120P000 |   1.46G |  120.0 |  7747 | 11.45M | 2499 |      8018 | 11.03M | 2012 |       822 | 422.78K |  487 | "31,41,51,61,71,81" | 0:13'16'' | 0:01'55'' |
| Q35L60X160P000 |   1.95G |  160.0 |  6698 | 11.44M | 2786 |      6923 | 10.97M | 2220 |       812 | 470.54K |  566 | "31,41,51,61,71,81" | 0:16'02'' | 0:01'52'' |

## s288c: merge anchors with Qxx and QxxL60Xxx

```bash
BASE_NAME=s288c
cd ${HOME}/data/anchr/${BASE_NAME}

# merge anchors with Qxx
for Q in 20 25 30 35; do
    mkdir -p mergeQ${Q}
    anchr contained \
        $(
            parallel -k --no-run-if-empty -j 6 '
                if [ -e Q{1}L{2}X{3}P{4}/anchor/pe.anchor.fa ]; then
                    echo Q{1}L{2}X{3}P{4}/anchor/pe.anchor.fa
                fi
                ' ::: ${Q} ::: 60 ::: 40 80 120 160 ::: 000 001 002 003 004 005
        ) \
        --len 1000 --idt 0.98 --proportion 0.99999 --parallel 16 \
        -o stdout \
        | faops filter -a 1000 -l 0 stdin mergeQ${Q}/anchor.contained.fasta
    anchr orient mergeQ${Q}/anchor.contained.fasta --len 1000 --idt 0.98 -o mergeQ${Q}/anchor.orient.fasta
    anchr merge mergeQ${Q}/anchor.orient.fasta --len 1000 --idt 0.999 -o mergeQ${Q}/anchor.merge0.fasta
    anchr contained mergeQ${Q}/anchor.merge0.fasta --len 1000 --idt 0.98 \
        --proportion 0.99 --parallel 16 -o stdout \
        | faops filter -a 1000 -l 0 stdin mergeQ${Q}/anchor.merge.fasta
done

# merge anchors with QxxL60Xxx
for Q in 20 25 30 35; do
    for X in 40 80; do
        mkdir -p mergeQ${Q}X${X}
        anchr contained \
            $(
                parallel -k --no-run-if-empty -j 6 '
                    if [ -e Q{1}L{2}X{3}P{4}/anchor/pe.anchor.fa ]; then
                        echo Q{1}L{2}X{3}P{4}/anchor/pe.anchor.fa
                    fi
                    ' ::: ${Q} ::: 60 ::: ${X} ::: 000 001 002 003 004 005
            ) \
            --len 1000 --idt 0.98 --proportion 0.99999 --parallel 16 \
            -o stdout \
            | faops filter -a 1000 -l 0 stdin mergeQ${Q}X${X}/anchor.contained.fasta
        anchr orient mergeQ${Q}X${X}/anchor.contained.fasta --len 1000 --idt 0.98 -o mergeQ${Q}X${X}/anchor.orient.fasta
        anchr merge mergeQ${Q}X${X}/anchor.orient.fasta --len 1000 --idt 0.999 -o mergeQ${Q}X${X}/anchor.merge0.fasta
        anchr contained mergeQ${Q}X${X}/anchor.merge0.fasta --len 1000 --idt 0.98 \
            --proportion 0.99 --parallel 16 -o stdout \
            | faops filter -a 1000 -l 0 stdin mergeQ${Q}X${X}/anchor.merge.fasta
    done
done

# quast
rm -fr 9_qa_mergeQX
quast --no-check --threads 16 \
    --eukaryote \
    -R 1_genome/genome.fa \
    mergeQ20/anchor.merge.fasta \
    mergeQ25/anchor.merge.fasta \
    mergeQ30/anchor.merge.fasta \
    mergeQ35/anchor.merge.fasta \
    mergeQ20X40/anchor.merge.fasta \
    mergeQ20X80/anchor.merge.fasta \
    mergeQ25X40/anchor.merge.fasta \
    mergeQ25X80/anchor.merge.fasta \
    mergeQ30X40/anchor.merge.fasta \
    mergeQ30X80/anchor.merge.fasta \
    mergeQ35X40/anchor.merge.fasta \
    mergeQ35X80/anchor.merge.fasta \
    1_genome/paralogs.fas \
    --label "mergeQ20,mergeQ25,mergeQ30,mergeQ35,mergeQ20X40,mergeQ20X80,mergeQ25X40,mergeQ25X80,mergeQ30X40,mergeQ30X80,mergeQ35X40,mergeQ35X80,paralogs" \
    -o 9_qa_mergeQX

```

## s288c: merge anchors

```bash
BASE_NAME=s288c
cd ${HOME}/data/anchr/${BASE_NAME}

# merge anchors
mkdir -p merge
anchr contained \
    $(
        parallel -k --no-run-if-empty -j 6 "
            if [ -e Q{1}L{2}X{3}P{4}/anchor/pe.anchor.fa ]; then
                echo Q{1}L{2}X{3}P{4}/anchor/pe.anchor.fa
            fi
            " ::: 25 30 ::: 60 ::: 40 80 120 160 ::: 000 001 002 003 004 005
    ) \
    --len 1000 --idt 0.98 --proportion 0.99999 --parallel 16 \
    -o stdout \
    | faops filter -a 1000 -l 0 stdin merge/anchor.contained.fasta
anchr orient merge/anchor.contained.fasta --len 1000 --idt 0.98 -o merge/anchor.orient.fasta
anchr merge merge/anchor.orient.fasta --len 1000 --idt 0.999 -o merge/anchor.merge0.fasta
anchr contained merge/anchor.merge0.fasta --len 1000 --idt 0.98 \
    --proportion 0.99 --parallel 16 -o stdout \
    | faops filter -a 1000 -l 0 stdin merge/anchor.merge1.fasta
faops order merge/anchor.merge1.fasta \
    <(faops size merge/anchor.merge1.fasta | sort -n -r -k2,2 | cut -f 1) \
    merge/anchor.merge.fasta

# No need for this step
#mkdir -p merge/anchor
#pushd merge/anchor
#anchr anchors \
#    ../anchor.merge.fasta \
#    ../../2_illumina/Q25L60/pe.cor.fa \
#    -p 16 \
#    -o anchors.sh
#bash anchors.sh
#popd

# merge others
mkdir -p merge
anchr contained \
    $(
        parallel -k --no-run-if-empty -j 6 "
            if [ -e Q{1}L{2}X{3}P{4}/anchor/pe.others.fa ]; then
                echo Q{1}L{2}X{3}P{4}/anchor/pe.others.fa
            fi
            " ::: 25 30 ::: 60 ::: 40 80 120 160 ::: 000 001 002 003 004 005
    ) \
    --len 1000 --idt 0.98 --proportion 0.99999 --parallel 16 \
    -o stdout \
    | faops filter -a 1000 -l 0 stdin merge/others.contained.fasta
anchr orient merge/others.contained.fasta --len 1000 --idt 0.98 -o merge/others.orient.fasta
anchr merge merge/others.orient.fasta --len 1000 --idt 0.999 -o stdout \
    | faops filter -a 1000 -l 0 stdin merge/others.merge.fasta

# anchor sort on ref
bash ~/Scripts/cpan/App-Anchr/share/sort_on_ref.sh merge/anchor.merge.fasta 1_genome/genome.fa merge/anchor.sort
nucmer -l 200 1_genome/genome.fa merge/anchor.sort.fa
mummerplot -png out.delta -p anchor.sort --large

# mummerplot files
rm *.[fr]plot
rm out.delta
rm *.gp
mv anchor.sort.png merge/

# quast
rm -fr 9_qa
quast --no-check --threads 16 \
    -R 1_genome/genome.fa \
    merge/anchor.merge.fasta \
    merge/others.merge.fasta \
    1_genome/paralogs.fas \
    --label "merge,others,paralogs" \
    -o 9_qa

```

## s288c: 3GS

```bash
BASE_NAME=s288c
REAL_G=12157105
cd ${HOME}/data/anchr/${BASE_NAME}

canu \
    -p ${BASE_NAME} -d canu-raw-20x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=${REAL_G} \
    -pacbio-raw 3_pacbio/pacbio.20x.fasta

canu \
    -p ${BASE_NAME} -d canu-raw-40x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=${REAL_G} \
    -pacbio-raw 3_pacbio/pacbio.40x.fasta

canu \
    -p ${BASE_NAME} -d canu-raw-80x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=${REAL_G} \
    -pacbio-raw 3_pacbio/pacbio.80x.fasta

canu \
    -p ${BASE_NAME} -d canu-trim-20x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=${REAL_G} \
    -pacbio-raw 3_pacbio/pacbio.20x.trim.fasta

canu \
    -p ${BASE_NAME} -d canu-trim-40x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=${REAL_G} \
    -pacbio-raw 3_pacbio/pacbio.40x.trim.fasta

canu \
    -p ${BASE_NAME} -d canu-trim-80x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=${REAL_G} \
    -pacbio-raw 3_pacbio/pacbio.80x.trim.fasta

# quast
rm -fr 9_qa_canu
quast --no-check --threads 16 \
    --eukaryote \
    -R 1_genome/genome.fa \
    canu-raw-20x/${BASE_NAME}.contigs.fasta \
    canu-trim-20x/${BASE_NAME}.contigs.fasta \
    canu-raw-40x/${BASE_NAME}.contigs.fasta \
    canu-trim-40x/${BASE_NAME}.contigs.fasta \
    canu-raw-80x/${BASE_NAME}.contigs.fasta \
    canu-trim-80x/${BASE_NAME}.contigs.fasta \
    1_genome/paralogs.fas \
    --label "20x,20x.trim,40x,40x.trim,80x,80x.trim,paralogs" \
    -o 9_qa_canu

find . -type d -name "correction" -path "*canu-*" | xargs rm -fr

faops n50 -S -C canu-raw-20x/${BASE_NAME}.trimmedReads.fasta.gz
faops n50 -S -C canu-trim-20x/${BASE_NAME}.trimmedReads.fasta.gz
faops n50 -S -C canu-raw-40x/${BASE_NAME}.trimmedReads.fasta.gz
faops n50 -S -C canu-trim-40x/${BASE_NAME}.trimmedReads.fasta.gz
faops n50 -S -C canu-raw-80x/${BASE_NAME}.trimmedReads.fasta.gz
faops n50 -S -C canu-trim-80x/${BASE_NAME}.trimmedReads.fasta.gz

minimap canu-raw-20x/${BASE_NAME}.contigs.fasta 1_genome/genome.fa \
    | minidot - > canu-raw-20x/minidot.eps

minimap canu-raw-40x/${BASE_NAME}.contigs.fasta 1_genome/genome.fa \
    | minidot - > canu-raw-40x/minidot.eps

minimap canu-raw-80x/${BASE_NAME}.contigs.fasta 1_genome/genome.fa \
    | minidot - > canu-raw-80x/minidot.eps

```

## s288c: local corrections

```bash
BASE_NAME=s288c
REAL_G=12157105
cd ${HOME}/data/anchr/${BASE_NAME}

rm -fr localCor
anchr overlap2 \
    --parallel 16 \
    merge/anchor.merge.fasta \
    3_pacbio/pacbio.40x.trim.fasta \
    -d localCor \
    -b 20 --len 1000 --idt 0.85 --all

pushd localCor

anchr cover \
    --range "1-$(faops n50 -H -N 0 -C anchor.fasta)" \
    --len 1000 --idt 0.85 -c 2 \
    anchorLong.ovlp.tsv \
    -o anchor.cover.json
cat anchor.cover.json | jq "." > environment.json

rm -fr group
anchr localcor \
    anchorLong.db \
    anchorLong.ovlp.tsv \
    --parallel 16 \
    --range $(cat environment.json | jq -r '.TRUSTED') \
    --len 1000 --idt 0.85 -v

faops some -i -l 0 \
    long.fasta \
    group/overlapped.long.txt \
    independentLong.fasta

find . -type d -name "correction" | xargs rm -fr

# localCor
gzip -d -c -f $(find group -type f -name "*.correctedReads.fasta.gz") \
    | faops filter -l 0 stdin stdout \
    | grep -E '^>long' -A 1 \
    | sed '/^--$/d' \
    | faops dazz -a -l 0 stdin stdout \
    | pigz -c > localCor.fasta.gz

canu \
    -p ${BASE_NAME} -d localCor \
    gnuplotTested=true \
    genomeSize=${REAL_G} \
    -pacbio-corrected localCor.fasta.gz \
    -pacbio-corrected anchor.fasta

canu \
    -p ${BASE_NAME} -d localCorRaw \
    gnuplotTested=true \
    genomeSize=${REAL_G} \
    -pacbio-raw localCor.fasta.gz \
    -pacbio-raw anchor.fasta

canu \
    -p ${BASE_NAME} -d localCorIndep \
    gnuplotTested=true \
    genomeSize=${REAL_G} \
    -pacbio-raw localCor.fasta.gz \
    -pacbio-raw anchor.fasta \
    -pacbio-raw independentLong.fasta

popd

# quast
rm -fr 9_qa_localCor
quast --no-check --threads 16 \
    --eukaryote \
    -R 1_genome/genome.fa \
    localCor/anchor.fasta \
    localCor/localCor/${BASE_NAME}.contigs.fasta \
    localCor/localCorRaw/${BASE_NAME}.contigs.fasta \
    localCor/localCorIndep/${BASE_NAME}.contigs.fasta \
    1_genome/paralogs.fas \
    --label "anchor,localCor,localCorRaw,localCorIndep,paralogs" \
    -o 9_qa_localCor

find . -type d -name "correction" | xargs rm -fr

```

## s288c: expand anchors

在酿酒酵母中, 有下列几组完全相同的序列, 它们都是新近发生的片段重复:

* I:216563-218385, VIII:537165-538987
* I:223713-224783, VIII:550350-551420
* IV:528442-530427, IV:532327-534312, IV:536212-538197
* IV:530324-531519, IV:534209-535404
* IV:5645-7725, X:738076-740156
* IV:7810-9432, X:736368-737990
* IX:9683-11043, X:9666-11026
* IV:1244112-1245373, XV:575980-577241
* VIII:212266-214124, VIII:214264-216122
* IX:11366-14953, X:11349-14936
* XII:468935-470576, XII:472587-474228, XII:482167-483808, XII:485819-487460,
* XII:483798-485798, XII:487450-489450

* anchorLong

```bash
BASE_NAME=s288c
cd ${HOME}/data/anchr/${BASE_NAME}

rm -fr anchorLong
anchr overlap2 \
    --parallel 16 \
    merge/anchor.merge.fasta \
    3_pacbio/pacbio.40x.trim.fasta \
    -d anchorLong \
    -b 20 --len 1000 --idt 0.85 --all

pushd anchorLong

anchr cover \
    --range "1-$(faops n50 -H -N 0 -C anchor.fasta)" \
    --len 1000 --idt 0.85 -c 2 \
    anchorLong.ovlp.tsv \
    -o anchor.cover.json
cat anchor.cover.json | jq "." > environment.json

anchr overlap \
    anchor.fasta \
    --serial --len 20 --idt 0.9999 \
    -o stdout \
    | perl -nla -e '
        BEGIN {

doc/model_organisms.md  view on Meta::CPAN 


```bash
BASE_NAME=s288c
cd ${HOME}/data/anchr/${BASE_NAME}

printf "| %s | %s | %s | %s |\n" \
    "Name" "N50" "Sum" "#" \
    > stat3.md
printf "|:--|--:|--:|--:|\n" >> stat3.md

printf "| %s | %s | %s | %s |\n" \
    $(echo "Genome";   faops n50 -H -S -C 1_genome/genome.fa;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "Paralogs";   faops n50 -H -S -C 1_genome/paralogs.fas;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "anchor.merge"; faops n50 -H -S -C merge/anchor.merge.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "others.merge"; faops n50 -H -S -C merge/others.merge.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "anchorLong"; faops n50 -H -S -C anchorLong/contig.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "contigTrim"; faops n50 -H -S -C contigTrim/contig.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "canu-raw"; faops n50 -H -S -C canu-raw-40x/${BASE_NAME}.contigs.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "canu-trim"; faops n50 -H -S -C canu-trim-40x/${BASE_NAME}.contigs.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "spades.contig"; faops n50 -H -S -C 8_spades/contigs.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "spades.scaffold"; faops n50 -H -S -C 8_spades/scaffolds.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "platanus.contig"; faops n50 -H -S -C 8_platanus/out_contig.fa;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "platanus.scaffold"; faops n50 -H -S -C 8_platanus/out_gapClosed.fa;) >> stat3.md

cat stat3.md
```

| Name              |    N50 |      Sum |    # |
|:------------------|-------:|---------:|-----:|
| Genome            | 924431 | 12157105 |   17 |
| Paralogs          |   3851 |  1059148 |  366 |
| anchor.merge      |  29017 | 11359547 |  665 |
| others.merge      |   2625 |   282212 |  127 |
| anchorLong        |  38821 | 11269708 |  478 |
| contigTrim        | 460244 | 11555366 |   37 |
| canu-raw          | 475272 | 12333950 |   41 |
| canu-trim         | 475066 | 12194521 |   36 |
| spades.contig     |  89836 | 11731746 | 1189 |
| spades.scaffold   |  98572 | 11732702 | 1167 |
| platanus.contig   |   5983 | 12437850 | 7727 |
| platanus.scaffold |  55443 | 12073445 | 4735 |

* quast

```bash
BASE_NAME=s288c
cd ${HOME}/data/anchr/${BASE_NAME}

rm -fr 9_qa_contig
quast --no-check --threads 16 \
    --eukaryote \
    -R 1_genome/genome.fa \
    merge/anchor.merge.fasta \
    anchorLong/contig.fasta \
    contigTrim/contig.fasta \
    canu-trim-40x/${BASE_NAME}.contigs.fasta \
    8_spades/scaffolds.fasta \
    8_platanus/out_gapClosed.fa \
    1_genome/paralogs.fas \
    --label "merge,contig,contigTrim,canu-40x,spades,platanus,paralogs" \
    -o 9_qa_contig

```

* Clear QxxLxxXxx.

```bash
BASE_NAME=s288c
cd ${HOME}/data/anchr/${BASE_NAME}

rm -fr 2_illumina/Q{20,25,30,35}L{30,60,90,120}X*
rm -fr Q{20,25,30,35}L{30,60,90,120}X*
```

# *Drosophila melanogaster* iso-1

* Genome: [Ensembl 82](http://sep2015.archive.ensembl.org/Drosophila_melanogaster/Info/Index)
* Proportion of paralogs (> 1000 bp): 0.0661

## iso_1: download

* Reference genome

```bash
mkdir -p ~/data/anchr/iso_1/1_genome
cd ~/data/anchr/iso_1/1_genome

wget -N ftp://ftp.ensembl.org/pub/release-82/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.dna_sm.toplevel.fa.gz
faops order Drosophila_melanogaster.BDGP6.dna_sm.toplevel.fa.gz \
    <(for chr in {2L,2R,3L,3R,4,X,Y,dmel_mitochondrion_genome}; do echo $chr; done) \
    genome.fa

cp ~/data/anchr/paralogs/model/Results/iso_1/iso_1.multi.fas 1_genome/paralogs.fas
```

* Illumina

    * [ERX645969](http://www.ebi.ac.uk/ena/data/view/ERX645969): ERR701706-ERR701711
    * SRR306628 labels ycnbwsp instead of iso-1.

```bash
mkdir -p ~/data/anchr/iso_1/2_illumina
cd ~/data/anchr/iso_1/2_illumina

cat << EOF > sra_ftp.txt
ftp://ftp.sra.ebi.ac.uk/vol1/err/ERR701/ERR701706
ftp://ftp.sra.ebi.ac.uk/vol1/err/ERR701/ERR701707
ftp://ftp.sra.ebi.ac.uk/vol1/err/ERR701/ERR701708
ftp://ftp.sra.ebi.ac.uk/vol1/err/ERR701/ERR701709
ftp://ftp.sra.ebi.ac.uk/vol1/err/ERR701/ERR701710

doc/model_organisms.md  view on Meta::CPAN 

| Q30L60X80P000 | 11.01G |   80.0 | 12544 | 120.37M | 20203 |     13096 | 115.53M | 15333 |       867 | 4.84M | 4870 | "31,41,43,45,51,61,71,81" | 2:35'52'' | 0:13'13'' |

## iso_1: merge anchors

```bash
BASE_NAME=iso_1
cd ${HOME}/data/anchr/${BASE_NAME}

# merge anchors
mkdir -p merge
anchr contained \
    $(
        parallel -k --no-run-if-empty -j 6 "
            if [ -e Q{1}L{2}X{3}P{4}/anchor/pe.anchor.fa ]; then
                echo Q{1}L{2}X{3}P{4}/anchor/pe.anchor.fa
            fi
            " ::: 25 30 ::: 60 ::: 40 80 ::: 000 001 002 003 004 005
    ) \
    --len 1000 --idt 0.98 --proportion 0.99999 --parallel 16 \
    -o stdout \
    | faops filter -a 1000 -l 0 stdin merge/anchor.contained.fasta
anchr orient merge/anchor.contained.fasta --len 1000 --idt 0.98 -o merge/anchor.orient.fasta
anchr merge merge/anchor.orient.fasta --len 1000 --idt 0.999 -o merge/anchor.merge0.fasta
anchr contained merge/anchor.merge0.fasta --len 1000 --idt 0.98 \
    --proportion 0.99 --parallel 16 -o stdout \
    | faops filter -a 1000 -l 0 stdin merge/anchor.merge1.fasta
faops order merge/anchor.merge1.fasta \
    <(faops size merge/anchor.merge1.fasta | sort -n -r -k2,2 | cut -f 1) \
    merge/anchor.merge.fasta

# merge others
mkdir -p merge
anchr contained \
    $(
        parallel -k --no-run-if-empty -j 6 "
            if [ -e Q{1}L{2}X{3}P{4}/anchor/pe.others.fa ]; then
                echo Q{1}L{2}X{3}P{4}/anchor/pe.others.fa
            fi
            " ::: 25 30 ::: 60 ::: 40 80 ::: 000 001 002 003 004 005
    ) \
    --len 1000 --idt 0.98 --proportion 0.99999 --parallel 16 \
    -o stdout \
    | faops filter -a 1000 -l 0 stdin merge/others.contained.fasta
anchr orient merge/others.contained.fasta --len 1000 --idt 0.98 -o merge/others.orient.fasta
anchr merge merge/others.orient.fasta --len 1000 --idt 0.999 -o stdout \
    | faops filter -a 1000 -l 0 stdin merge/others.merge.fasta

# anchor sort on ref
bash ~/Scripts/cpan/App-Anchr/share/sort_on_ref.sh merge/anchor.merge.fasta 1_genome/genome.fa merge/anchor.sort
nucmer -l 200 1_genome/genome.fa merge/anchor.sort.fa
mummerplot -png out.delta -p anchor.sort --large

# mummerplot files
rm *.[fr]plot
rm out.delta
rm *.gp
mv anchor.sort.png merge/

# quast
rm -fr 9_qa
quast --no-check --threads 16 \
    --eukaryote \
    --no-icarus \
    -R 1_genome/genome.fa \
    merge/anchor.merge.fasta \
    merge/others.merge.fasta \
    1_genome/paralogs.fas \
    --label "merge,others,paralogs" \
    -o 9_qa

```

## iso_1: 3GS

```bash
BASE_NAME=iso_1
REAL_G=137567477
cd ${HOME}/data/anchr/${BASE_NAME}

canu \
    -p ${BASE_NAME} -d canu-raw-40x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=${REAL_G} \
    -pacbio-raw 3_pacbio/pacbio.40x.fasta

canu \
    -p ${BASE_NAME} -d canu-trim-40x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=${REAL_G} \
    -pacbio-raw 3_pacbio/pacbio.40x.trim.fasta

find . -type d -name "correction" -path "*canu-*" | xargs rm -fr

minimap canu-raw-40x/${BASE_NAME}.contigs.fasta 1_genome/genome.fa \
    | minidot - > canu-raw-40x/minidot.eps

minimap canu-trim-40x/${BASE_NAME}.contigs.fasta 1_genome/genome.fa \
    | minidot - > canu-trim-40x/minidot.eps

faops n50 -S -C canu-raw-40x/${BASE_NAME}.trimmedReads.fasta.gz
faops n50 -S -C canu-trim-40x/${BASE_NAME}.trimmedReads.fasta.gz

```

## iso_1: expand anchors

* anchorLong

```bash
BASE_NAME=iso_1
cd ${HOME}/data/anchr/${BASE_NAME}

rm -fr anchorLong
anchr overlap2 \
    --parallel 16 \
    merge/anchor.merge.fasta \
    3_pacbio/pacbio.40x.trim.fasta \
    -d anchorLong \
    -b 50 --len 1000 --idt 0.85 --all

pushd anchorLong

doc/model_organisms.md  view on Meta::CPAN 

```

## iso_1: final stats

* Stats

```bash
BASE_NAME=iso_1
cd ${HOME}/data/anchr/${BASE_NAME}

printf "| %s | %s | %s | %s |\n" \
    "Name" "N50" "Sum" "#" \
    > stat3.md
printf "|:--|--:|--:|--:|\n" >> stat3.md

printf "| %s | %s | %s | %s |\n" \
    $(echo "Genome";   faops n50 -H -S -C 1_genome/genome.fa;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "Paralogs";   faops n50 -H -S -C 1_genome/paralogs.fas;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "anchor.merge"; faops n50 -H -S -C merge/anchor.merge.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "others.merge"; faops n50 -H -S -C merge/others.merge.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "anchorLong"; faops n50 -H -S -C anchorLong/contig.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "contigTrim"; faops n50 -H -S -C contigTrim/contig.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "spades.contig"; faops n50 -H -S -C 8_spades/contigs.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "spades.scaffold"; faops n50 -H -S -C 8_spades/scaffolds.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "platanus.contig"; faops n50 -H -S -C 8_platanus/out_contig.fa;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "platanus.scaffold"; faops n50 -H -S -C 8_platanus/out_gapClosed.fa;) >> stat3.md

cat stat3.md
```

| Name              |      N50 |       Sum |      # |
|:------------------|---------:|----------:|-------:|
| Genome            | 25286936 | 137567477 |      8 |
| Paralogs          |     4031 |  13665900 |   4492 |
| anchor.merge      |    26860 | 117041459 |   9566 |
| others.merge      |     8732 |   3092289 |   1004 |
| anchor.cover      |    26199 | 116199529 |   9576 |
| anchorLong        |    69814 | 115806088 |   4924 |
| contigTrim        |  1238480 | 123572499 |    603 |
| spades.contig     |   108756 | 132705321 |  61620 |
| spades.scaffold   |   142273 | 132725706 |  61182 |
| platanus.contig   |    11503 | 156820565 | 359399 |
| platanus.scaffold |   146404 | 129134232 |  71416 |

* quast

```bash
BASE_NAME=iso_1
cd ${HOME}/data/anchr/${BASE_NAME}

rm -fr 9_qa_contig
quast --no-check --threads 16 \
    --eukaryote \
    --no-icarus \
    -R 1_genome/genome.fa \
    merge/anchor.merge.fasta \
    anchorLong/contig.fasta \
    contigTrim/contig.fasta \
    canu-raw-40x/${BASE_NAME}.contigs.fasta \
    canu-trim-40x/${BASE_NAME}.contigs.fasta \
    8_spades/scaffolds.fasta \
    8_platanus/out_gapClosed.fa \
    1_genome/paralogs.fas \
    --label "merge,contig,contigTrim,canu-40x,canu-40x.trim,spades,platanus,paralogs" \
    -o 9_qa_contig

```

* Clear QxxLxxXxx.

```bash
BASE_NAME=iso_1
cd ${HOME}/data/anchr/${BASE_NAME}

rm -fr 2_illumina/Q{20,25,30,35}L{30,60,90,120}X*
rm -fr Q{20,25,30,35}L{30,60,90,120}X*
```

# *Caenorhabditis elegans* N2

* Genome: [Ensembl 82](http://sep2015.archive.ensembl.org/Caenorhabditis_elegans/Info/Index)
* Proportion of paralogs (> 1000 bp): 0.0472

## n2: download

* Reference genome

```bash
mkdir -p ~/data/anchr/n2/1_genome
cd ~/data/anchr/n2/1_genome

wget -N ftp://ftp.ensembl.org/pub/release-82/fasta/caenorhabditis_elegans/dna/Caenorhabditis_elegans.WBcel235.dna_sm.toplevel.fa.gz
faops order Caenorhabditis_elegans.WBcel235.dna_sm.toplevel.fa.gz \
    <(for chr in {I,II,III,IV,V,X,MtDNA}; do echo $chr; done) \
    genome.fa

cp ~/data/anchr/paralogs/model/Results/n2/n2.multi.fas 1_genome/paralogs.fas
```

* Illumina

    * Other SRA
        * SRX770040 - [insert size](https://www.ncbi.nlm.nih.gov/sra/SRX770040[accn]) is 500-600 bp
        * ERR1039478 - adaptor contamination "ACTTCCAGGGATTTATAAGCCGATGACGTCATAACATCCCTGACCCTTTA"
        * DRR008443
        * SRR065390

```bash
# Downloading from ena with aria2
mkdir -p ~/data/anchr/n2/2_illumina
cd ~/data/anchr/n2/2_illumina

doc/model_organisms.md  view on Meta::CPAN 

| Q25L60X60P000 |  6.02G |   60.0 | 11787 | 99.24M | 19543 |     12467 | 88.53M | 12969 |      4629 | 10.71M | 6574 | "31,41,51,61,71,81" | 1:25'03'' | 0:08'23'' |
| Q30L60X30P000 |  3.01G |   30.0 | 10914 | 97.81M | 22843 |     11752 | 85.35M | 13764 |      1510 | 12.46M | 9079 | "31,41,51,61,71,81" | 0:59'47'' | 0:07'06'' |
| Q30L60X30P001 |  3.01G |   30.0 | 10160 | 97.39M | 24052 |     10924 | 84.51M | 14218 |      1255 | 12.87M | 9834 | "31,41,51,61,71,81" | 0:45'09'' | 0:07'05'' |
| Q30L60X60P000 |  6.02G |   60.0 | 12462 |  99.3M | 19363 |     12943 | 88.29M | 12773 |      5901 | 11.01M | 6590 | "31,41,51,61,71,81" | 0:59'46'' | 0:08'02'' |

## n2: merge anchors

```bash
BASE_NAME=n2
cd ${HOME}/data/anchr/${BASE_NAME}

# merge anchors
mkdir -p merge
anchr contained \
    $(
        parallel -k --no-run-if-empty -j 6 "
            if [ -e Q{1}L{2}X{3}P{4}/anchor/pe.anchor.fa ]; then
                echo Q{1}L{2}X{3}P{4}/anchor/pe.anchor.fa
            fi
            " ::: 25 30 ::: 60 ::: 30 60 ::: 000 001 002 003 004 005
    ) \
    --len 1000 --idt 0.98 --proportion 0.99999 --parallel 16 \
    -o stdout \
    | faops filter -a 1000 -l 0 stdin merge/anchor.contained.fasta
anchr orient merge/anchor.contained.fasta --len 1000 --idt 0.98 -o merge/anchor.orient.fasta
anchr merge merge/anchor.orient.fasta --len 1000 --idt 0.999 -o merge/anchor.merge0.fasta
anchr contained merge/anchor.merge0.fasta --len 1000 --idt 0.98 \
    --proportion 0.99 --parallel 16 -o stdout \
    | faops filter -a 1000 -l 0 stdin merge/anchor.merge.fasta

# merge others
mkdir -p merge
anchr contained \
    $(
        parallel -k --no-run-if-empty -j 6 "
            if [ -e Q{1}L{2}X{3}P{4}/anchor/pe.others.fa ]; then
                echo Q{1}L{2}X{3}P{4}/anchor/pe.others.fa
            fi
            " ::: 25 30 ::: 60 ::: 30 60 ::: 000 001 002 003 004 005
    ) \
    --len 1000 --idt 0.98 --proportion 0.99999 --parallel 16 \
    -o stdout \
    | faops filter -a 1000 -l 0 stdin merge/others.contained.fasta
anchr orient merge/others.contained.fasta --len 1000 --idt 0.98 -o merge/others.orient.fasta
anchr merge merge/others.orient.fasta --len 1000 --idt 0.999 -o stdout \
    | faops filter -a 1000 -l 0 stdin merge/others.merge.fasta

# anchor sort on ref
bash ~/Scripts/cpan/App-Anchr/share/sort_on_ref.sh merge/anchor.merge.fasta 1_genome/genome.fa merge/anchor.sort
nucmer -l 200 1_genome/genome.fa merge/anchor.sort.fa
mummerplot -png out.delta -p anchor.sort --large

# mummerplot files
rm *.[fr]plot
rm out.delta
rm *.gp
mv anchor.sort.png merge/

# quast
rm -fr 9_qa
quast --no-check --threads 16 \
    --eukaryote \
    --no-icarus \
    -R 1_genome/genome.fa \
    merge/anchor.merge.fasta \
    merge/others.merge.fasta \
    1_genome/paralogs.fas \
    --label "merge,others,paralogs" \
    -o 9_qa

```

## n2: 3GS

```bash
BASE_NAME=n2
REAL_G=100286401
cd ${HOME}/data/anchr/${BASE_NAME}

canu \
    -p ${BASE_NAME} -d canu-raw-40x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=${REAL_G} \
    -pacbio-raw 3_pacbio/pacbio.40x.fasta
    
canu \
    -p ${BASE_NAME} -d canu-raw-80x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=${REAL_G} \
    -pacbio-raw 3_pacbio/pacbio.80x.fasta

canu \
    -p ${BASE_NAME} -d canu-trim-40x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=${REAL_G} \
    -pacbio-raw 3_pacbio/pacbio.40x.trim.fasta
    
canu \
    -p ${BASE_NAME} -d canu-trim-80x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=${REAL_G} \
    -pacbio-raw 3_pacbio/pacbio.80x.trim.fasta

find . -type d -name "correction" -path "*canu-*" | xargs rm -fr

minimap canu-raw-40x/${BASE_NAME}.contigs.fasta 1_genome/genome.fa \
    | minidot - > canu-raw-40x/minidot.eps

minimap canu-trim-40x/${BASE_NAME}.contigs.fasta 1_genome/genome.fa \
    | minidot - > canu-trim-40x/minidot.eps

faops n50 -S -C canu-raw-40x/${BASE_NAME}.trimmedReads.fasta.gz
faops n50 -S -C canu-trim-40x/${BASE_NAME}.trimmedReads.fasta.gz
faops n50 -S -C canu-raw-80x/${BASE_NAME}.trimmedReads.fasta.gz
faops n50 -S -C canu-trim-80x/${BASE_NAME}.trimmedReads.fasta.gz

```

## n2: expand anchors

* anchorLong

doc/model_organisms.md  view on Meta::CPAN 

## n2: final stats

* Stats

```bash
BASE_NAME=n2
cd ${HOME}/data/anchr/${BASE_NAME}

printf "| %s | %s | %s | %s |\n" \
    "Name" "N50" "Sum" "#" \
    > stat3.md
printf "|:--|--:|--:|--:|\n" >> stat3.md

printf "| %s | %s | %s | %s |\n" \
    $(echo "Genome";   faops n50 -H -S -C 1_genome/genome.fa;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "Paralogs";   faops n50 -H -S -C 1_genome/paralogs.fas;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "anchor.merge"; faops n50 -H -S -C merge/anchor.merge.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "others.merge"; faops n50 -H -S -C merge/others.merge.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "anchor.cover"; faops n50 -H -S -C merge/anchor.cover.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "anchorLong"; faops n50 -H -S -C anchorLong/contig.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "contigTrim"; faops n50 -H -S -C contigTrim/contig.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "spades.contig"; faops n50 -H -S -C 8_spades/contigs.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "spades.scaffold"; faops n50 -H -S -C 8_spades/scaffolds.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "platanus.contig"; faops n50 -H -S -C 8_platanus/out_contig.fa;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "platanus.scaffold"; faops n50 -H -S -C 8_platanus/out_gapClosed.fa;) >> stat3.md

cat stat3.md
```

| Name              |      N50 |       Sum |      # |
|:------------------|---------:|----------:|-------:|
| Genome            | 17493829 | 100286401 |      7 |
| Paralogs          |     2013 |   5313653 |   2637 |
| anchor.merge      |    15525 |  90530693 |  11777 |
| others.merge      |    10805 |  11087395 |   3278 |
| anchor.cover      |    15486 |  90231476 |  11704 |
| anchorLong        |    22963 |  89834518 |   8438 |
| contigTrim        |   335060 |  95965683 |    607 |
| spades.contig     |    34792 | 105621949 |  39732 |
| spades.scaffold   |    39185 | 105667774 |  39154 |
| platanus.contig   |     9540 | 108908253 | 143264 |
| platanus.scaffold |    28158 |  99589056 |  35182 |

* quast

```bash
BASE_NAME=n2
cd ${HOME}/data/anchr/${BASE_NAME}

rm -fr 9_qa_contig
quast --no-check --threads 16 \
    --eukaryote \
    --no-icarus \
    -R 1_genome/genome.fa \
    merge/anchor.merge.fasta \
    merge/anchor.cover.fasta \
    anchorLong/contig.fasta \
    contigTrim/contig.fasta \
    canu-raw-40x/${BASE_NAME}.contigs.fasta \
    8_spades/scaffolds.fasta \
    8_platanus/out_gapClosed.fa \
    1_genome/paralogs.fas \
    --label "merge,cover,contig,contigTrim,canu-40x,spades,platanus,paralogs" \
    -o 9_qa_contig

```

* Clear QxxLxxx.

```bash
BASE_DIR=$HOME/data/anchr/n2
cd ${BASE_DIR}

rm -fr 2_illumina/Q{20,25,30,35}L{30,60,90,120}X*
rm -fr Q{20,25,30,35}L{30,60,90,120}X*
```

# *Arabidopsis thaliana* Col-0

* Genome: [Ensembl Genomes](http://plants.ensembl.org/Arabidopsis_thaliana/Info/Index)
* Proportion of paralogs (> 1000 bp): 0.1158

## col_0: download

* Reference genome

```bash
mkdir -p ~/data/anchr/col_0/1_genome
cd ~/data/anchr/col_0/1_genome
wget -N ftp://ftp.ensemblgenomes.org/pub/release-29/plants/fasta/arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.29.dna_sm.toplevel.fa.gz
faops order Arabidopsis_thaliana.TAIR10.29.dna_sm.toplevel.fa.gz \
    <(for chr in {1,2,3,4,5,Mt,Pt}; do echo $chr; done) \
    genome.fa
```

* Illumina HiSeq (100 bp)

    [SRX202246](https://www.ncbi.nlm.nih.gov/sra/SRX202246[accn])

```bash
# Downloading from ena with aria2
mkdir -p ~/data/anchr/col_0/2_illumina
cd ~/data/anchr/col_0/2_illumina

cat << EOF > sra_ftp.txt
ftp://ftp.sra.ebi.ac.uk/vol1/srr/SRR611/SRR611086
ftp://ftp.sra.ebi.ac.uk/vol1/srr/SRR616/SRR616966
EOF

aria2c -x 9 -s 3 -c -i sra_ftp.txt

doc/model_organisms.md  view on Meta::CPAN 


```bash
BASE_NAME=col_0
cd ${HOME}/data/anchr/${BASE_NAME}

# merge anchors
mkdir -p merge
anchr contained \
    $(
        parallel -k --no-run-if-empty -j 6 "
            if [ -e Q{1}L{2}X{3}P{4}/anchor/pe.anchor.fa ]; then
                echo Q{1}L{2}X{3}P{4}/anchor/pe.anchor.fa
            fi
            " ::: 25 30 ::: 60 ::: 30 60 ::: 000 001 002 003 004 005
    ) \
    --len 1000 --idt 0.98 --proportion 0.99999 --parallel 16 \
    -o stdout \
    | faops filter -a 1000 -l 0 stdin merge/anchor.contained.fasta
anchr orient merge/anchor.contained.fasta \
    --len 1000 --idt 0.98 --parallel 16 \
    -o merge/anchor.orient.fasta
anchr merge merge/anchor.orient.fasta \
    --len 1000 --idt 0.999 --parallel 16 \
    -o merge/anchor.merge0.fasta
anchr contained merge/anchor.merge0.fasta \
    --len 1000 --idt 0.98 --proportion 0.99 --parallel 16 -o stdout \
    | faops filter -a 1000 -l 0 stdin merge/anchor.merge.fasta

# merge others
anchr contained \
    $(
        parallel -k --no-run-if-empty -j 6 "
            if [ -e Q{1}L{2}X{3}P{4}/anchor/pe.others.fa ]; then
                echo Q{1}L{2}X{3}P{4}/anchor/pe.others.fa
            fi
            " ::: 25 30 ::: 60 ::: 30 60 ::: 000 001 002 003 004 005
    ) \
    --len 1000 --idt 0.98 --proportion 0.99999 --parallel 16 \
    -o stdout \
    | faops filter -a 1000 -l 0 stdin merge/others.contained.fasta
anchr orient merge/others.contained.fasta --len 1000 --idt 0.98 -o merge/others.orient.fasta
anchr merge merge/others.orient.fasta --len 1000 --idt 0.999 -o stdout \
    | faops filter -a 1000 -l 0 stdin merge/others.merge.fasta

# anchor sort on ref
bash ~/Scripts/cpan/App-Anchr/share/sort_on_ref.sh merge/anchor.merge.fasta 1_genome/genome.fa merge/anchor.sort

# mummerplot files
nucmer -l 200 1_genome/genome.fa merge/anchor.sort.fa
mummerplot out.delta --png --large -p anchor.sort
rm *.[fr]plot
rm out.delta
rm *.gp
mv anchor.sort.png merge/

# minidot
minimap 1_genome/genome.fa merge/anchor.sort.fa | minidot - > merge/anchor.minidot.eps

# quast
rm -fr 9_qa
quast --no-check --threads 16 \
    --eukaryote \
    --no-icarus \
    -R 1_genome/genome.fa \
    merge/anchor.merge.fasta \
    merge/others.merge.fasta \
    1_genome/paralogs.fas \
    --label "merge,others,paralogs" \
    -o 9_qa

```

## col_0: 3GS

```bash
BASE_NAME=col_0
REAL_G=119667750
cd ${HOME}/data/anchr/${BASE_NAME}

canu \
    -p ${BASE_NAME} -d canu-raw-40x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=${REAL_G} \
    -pacbio-raw 3_pacbio/pacbio.40x.fasta

canu \
    -p ${BASE_NAME} -d canu-raw-80x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=${REAL_G} \
    -pacbio-raw 3_pacbio/pacbio.80x.fasta

canu \
    -p ${BASE_NAME} -d canu-trim-80x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=${REAL_G} \
    -pacbio-raw 3_pacbio/pacbio.80x.trim.fasta

faops n50 -S -C canu-raw-40x/${BASE_NAME}.trimmedReads.fasta.gz
faops n50 -S -C canu-raw-80x/${BASE_NAME}.trimmedReads.fasta.gz
faops n50 -S -C canu-trim-80x/${BASE_NAME}.trimmedReads.fasta.gz

rm -fr canu-raw-40x/correction
rm -fr canu-raw-80x/correction
rm -fr canu-trim-80x/correction

```

## col_0: expand anchors

* anchorLong

```bash
BASE_NAME=col_0
cd ${HOME}/data/anchr/${BASE_NAME}

anchr cover \
    --parallel 16 \
    -c 2 -m 40 \
    -b 50 --len 1000 --idt 0.9 \
    merge/anchor.merge.fasta \
    canu-trim-80x/${BASE_NAME}.trimmedReads.fasta.gz \

doc/model_organisms.md  view on Meta::CPAN 


```bash
BASE_NAME=col_0
cd ${HOME}/data/anchr/${BASE_NAME}

printf "| %s | %s | %s | %s |\n" \
    "Name" "N50" "Sum" "#" \
    > stat3.md
printf "|:--|--:|--:|--:|\n" >> stat3.md

printf "| %s | %s | %s | %s |\n" \
    $(echo "Genome";   faops n50 -H -S -C 1_genome/genome.fa;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "Paralogs";   faops n50 -H -S -C 1_genome/paralogs.fas;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "anchor.merge"; faops n50 -H -S -C merge/anchor.merge.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "others.merge"; faops n50 -H -S -C merge/others.merge.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "anchor.cover"; faops n50 -H -S -C merge/anchor.cover.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "anchorLong"; faops n50 -H -S -C anchorLong/contig.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "contigTrim"; faops n50 -H -S -C contigTrim/contig.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "canu-trim"; faops n50 -H -S -C canu-trim-80x/${BASE_NAME}.contigs.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "spades.contig"; faops n50 -H -S -C 8_spades/contigs.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "spades.scaffold"; faops n50 -H -S -C 8_spades/scaffolds.fasta;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "platanus.contig"; faops n50 -H -S -C 8_platanus/out_contig.fa;) >> stat3.md
printf "| %s | %s | %s | %s |\n" \
    $(echo "platanus.scaffold"; faops n50 -H -S -C 8_platanus/out_gapClosed.fa;) >> stat3.md

cat stat3.md
```

| Name              |      N50 |       Sum |      # |
|:------------------|---------:|----------:|-------:|
| Genome            | 23459830 | 119667750 |      7 |
| Paralogs          |     2007 |  16447809 |   8055 |
| anchor.merge      |    28391 | 108282399 |   8601 |
| others.merge      |     2939 |   2073808 |    882 |
| anchor.cover      |    28398 | 107735288 |   8339 |
| anchorLong        |    45080 | 107528125 |   5622 |
| contigTrim        |   694603 | 108985292 |    666 |
| canu-trim         |  2880862 | 119217587 |    244 |
| spades.contig     |    55516 | 154715185 | 115087 |
| spades.scaffold   |    67856 | 154750615 | 114703 |
| platanus.contig   |    15019 | 139807772 | 106870 |
| platanus.scaffold |   192019 | 128497152 |  67429 |

* quast

```bash
BASE_NAME=col_0
cd ${HOME}/data/anchr/${BASE_NAME}

rm -fr 9_qa_contig
quast --no-check --threads 16 \
    --eukaryote \
    --no-icarus \
    -R 1_genome/genome.fa \
    merge/anchor.merge.fasta \
    merge/anchor.cover.fasta \
    anchorLong/contig.fasta \
    contigTrim/contig.fasta \
    canu-trim-80x/${BASE_NAME}.contigs.fasta \
    1_genome/paralogs.fas \
    --label "merge,cover,contig,contigTrim,canu-trim,paralogs" \
    -o 9_qa_contig

```

* Clear QxxLxxx.

```bash
BASE_DIR=$HOME/data/anchr/col_0
cd ${BASE_DIR}

rm -fr 2_illumina/Q{20,25,30,35}L{30,60,90,120}X*
rm -fr Q{20,25,30,35}L{30,60,90,120}X*
```



( run in 1.405 second using v1.01-cache-2.11-cpan-39bf76dae61 )