App-Anchr

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doc/bacteria_2_3.md  view on Meta::CPAN

# Bacteria 2+3

[TOC levels=1-3]: # " "
- [Bacteria 2+3](#bacteria-23)
- [Escherichia virus Lambda](#escherichia-virus-lambda)
    - [lambda: download](#lambda-download)
    - [lambda: preprocess PacBio reads](#lambda-preprocess-pacbio-reads)
    - [lambda: reads stats](#lambda-reads-stats)
    - [lambda: 3GS](#lambda-3gs)
- [Shigella flexneri NCTC0001, 福氏志贺氏菌](#shigella-flexneri-nctc0001-福氏志贺氏菌)
    - [Sfle: download](#sfle-download)
    - [Sfle: combinations of different quality values and read lengths](#sfle-combinations-of-different-quality-values-and-read-lengths)
    - [Sfle: down sampling](#sfle-down-sampling)
    - [Sfle: generate super-reads](#sfle-generate-super-reads)
    - [Sfle: create anchors](#sfle-create-anchors)
    - [Sfle: results](#sfle-results)
    - [Sfle: merge anchors](#sfle-merge-anchors)
    - [Sfle: 3GS](#sfle-3gs)
    - [Sfle: expand anchors](#sfle-expand-anchors)
- [Vibrio parahaemolyticus ATCC BAA-239, 副溶血弧菌](#vibrio-parahaemolyticus-atcc-baa-239-副溶血弧菌)
    - [Vpar: download](#vpar-download)
    - [Vpar: combinations of different quality values and read lengths](#vpar-combinations-of-different-quality-values-and-read-lengths)
    - [Vpar: down sampling](#vpar-down-sampling)
    - [Vpar: generate super-reads](#vpar-generate-super-reads)
    - [Vpar: create anchors](#vpar-create-anchors)
    - [Vpar: results](#vpar-results)
    - [Vpar: merge anchors](#vpar-merge-anchors)
    - [Vpar: 3GS](#vpar-3gs)
    - [Vpar: expand anchors](#vpar-expand-anchors)
- [Legionella pneumophila subsp. pneumophila ATCC 33152D-5; Philadelphia-1, 嗜肺军团菌](#legionella-pneumophila-subsp-pneumophila-atcc-33152d-5-philadelphia-1-嗜肺军团菌)
    - [Lpne: download](#lpne-download)
    - [Lpne: combinations of different quality values and read lengths](#lpne-combinations-of-different-quality-values-and-read-lengths)
    - [Lpne: down sampling](#lpne-down-sampling)
    - [Lpne: generate super-reads](#lpne-generate-super-reads)
    - [Lpne: create anchors](#lpne-create-anchors)
    - [Lpne: results](#lpne-results)
    - [Lpne: merge anchors](#lpne-merge-anchors)
    - [Lpne: 3GS](#lpne-3gs)
    - [Lpne: expand anchors](#lpne-expand-anchors)
- [Neisseria gonorrhoeae FDAARGOS_207, 淋病奈瑟氏菌](#neisseria-gonorrhoeae-fdaargos-207-淋病奈瑟氏菌)
    - [Ngon: download](#ngon-download)
    - [Ngon: combinations of different quality values and read lengths](#ngon-combinations-of-different-quality-values-and-read-lengths)
    - [Ngon: down sampling](#ngon-down-sampling)
    - [Ngon: generate super-reads](#ngon-generate-super-reads)
    - [Ngon: create anchors](#ngon-create-anchors)
    - [Ngon: results](#ngon-results)
    - [Ngon: merge anchors](#ngon-merge-anchors)
    - [Ngon: 3GS](#ngon-3gs)
    - [Ngon: expand anchors](#ngon-expand-anchors)
- [Neisseria meningitidis FDAARGOS_209, 脑膜炎奈瑟氏菌](#neisseria-meningitidis-fdaargos-209-脑膜炎奈瑟氏菌)
    - [Nmen: download](#nmen-download)
    - [Nmen: combinations of different quality values and read lengths](#nmen-combinations-of-different-quality-values-and-read-lengths)
    - [Nmen: quorum](#nmen-quorum)
    - [Nmen: down sampling](#nmen-down-sampling)
    - [Nmen: k-unitigs and anchors (sampled)](#nmen-k-unitigs-and-anchors-sampled)
    - [Nmen: merge anchors](#nmen-merge-anchors)
    - [Nmen: 3GS](#nmen-3gs)
    - [Nmen: expand anchors](#nmen-expand-anchors)
- [Bordetella pertussis FDAARGOS_195, 百日咳博德特氏杆菌](#bordetella-pertussis-fdaargos-195-百日咳博德特氏杆菌)
    - [Bper: download](#bper-download)
    - [Bper: combinations of different quality values and read lengths](#bper-combinations-of-different-quality-values-and-read-lengths)
    - [Bper: down sampling](#bper-down-sampling)
    - [Bper: generate super-reads](#bper-generate-super-reads)
    - [Bper: create anchors](#bper-create-anchors)
    - [Bper: results](#bper-results)
    - [Bper: merge anchors](#bper-merge-anchors)
- [Corynebacterium diphtheriae FDAARGOS_197, 白喉杆菌](#corynebacterium-diphtheriae-fdaargos-197-白喉杆菌)
    - [Cdip: download](#cdip-download)
    - [Cdip: combinations of different quality values and read lengths](#cdip-combinations-of-different-quality-values-and-read-lengths)
    - [Cdip: quorum](#cdip-quorum)
    - [Cdip: down sampling](#cdip-down-sampling)
    - [Cdip: k-unitigs and anchors (sampled)](#cdip-k-unitigs-and-anchors-sampled)
    - [Cdip: merge anchors](#cdip-merge-anchors)
    - [Cdip: 3GS](#cdip-3gs)
    - [Cdip: expand anchors](#cdip-expand-anchors)
- [Francisella tularensis FDAARGOS_247, 土拉热弗朗西斯氏菌](#francisella-tularensis-fdaargos-247-土拉热弗朗西斯氏菌)
    - [Ftul: download](#ftul-download)
    - [Ftul: combinations of different quality values and read lengths](#ftul-combinations-of-different-quality-values-and-read-lengths)
    - [Ftul: quorum](#ftul-quorum)
    - [Ftul: down sampling](#ftul-down-sampling)
    - [Ftul: k-unitigs and anchors (sampled)](#ftul-k-unitigs-and-anchors-sampled)
    - [Ftul: merge anchors](#ftul-merge-anchors)
    - [Ftul: 3GS](#ftul-3gs)
    - [Ftul: expand anchors](#ftul-expand-anchors)
- [Haemophilus influenzae FDAARGOS_199, 流感嗜血杆菌](#haemophilus-influenzae-fdaargos-199-流感嗜血杆菌)
    - [Hinf: download](#hinf-download)
- [Listeria monocytogenes FDAARGOS_351, 单核细胞增生李斯特氏菌](#listeria-monocytogenes-fdaargos-351-单核细胞增生李斯特氏菌)
    - [Lmon: download](#lmon-download)
- [Clostridioides difficile 630](#clostridioides-difficile-630)
    - [Cdif: download](#cdif-download)
- [Campylobacter jejuni subsp. jejuni ATCC 700819, 空肠弯曲杆菌](#campylobacter-jejuni-subsp-jejuni-atcc-700819-空肠弯曲杆菌)
    - [Cjej: download](#cjej-download)


# Escherichia virus Lambda

Project
[SRP055199](https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP055199)

## lambda: download

* Reference genome

    * Strain: Escherichia virus Lambda (viruses)
    * Taxid: [10710](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=10710&lvl=3&lin=f&keep=1&srchmode=1&unlock)
    * RefSeq assembly accession:
      [GCF_000840245.1](ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/840/245/GCF_000840245.1_ViralProj14204/GCF_000840245.1_ViralProj14204_assembly_report.txt)
    * Proportion of paralogs (> 1000 bp): 0.0

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

aria2c -x 9 -s 3 -c ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/840/245/GCF_000840245.1_ViralProj14204/GCF_000840245.1_ViralProj14204_genomic.fna.gz

TAB=$'\t'
cat <<EOF > replace.tsv
NC_001416.1${TAB}1
EOF

faops replace GCF_000840245.1_ViralProj14204_genomic.fna.gz replace.tsv genome.fa

#cp ~/data/anchr/paralogs/otherbac/Results/lambda/lambda.multi.fas paralogs.fas

```

* PacBio

```bash
mkdir -p ~/data/anchr/lambda/3_pacbio
cd ~/data/anchr/lambda/3_pacbio

cat << EOF > sra_ftp.txt
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR179/005/SRR1796325/SRR1796325.fastq.gz
EOF

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

cat << EOF > sra_md5.txt
2c663d7ea426eea0aaba9017e1a9168c SRR1796325.fastq.gz
EOF

md5sum --check sra_md5.txt

doc/bacteria_2_3.md  view on Meta::CPAN

    Q20L60/anchor/pe.others.fa \
    Q20L90/anchor/pe.others.fa \
    Q25L60/anchor/pe.others.fa \
    Q25L90/anchor/pe.others.fa \
    Q30L60/anchor/pe.others.fa \
    Q30L90/anchor/pe.others.fa \
    --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

# 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

```

## Sfle: 3GS

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

canu \
    -p Sfle -d canu-raw-40x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=4.8m \
    -pacbio-raw 3_pacbio/pacbio.40x.fasta

canu \
    -p Sfle -d canu-raw-80x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=4.8m \
    -pacbio-raw 3_pacbio/pacbio.80x.fasta

faops n50 -S -C canu-raw-40x/Sfle.trimmedReads.fasta.gz
faops n50 -S -C canu-raw-80x/Sfle.trimmedReads.fasta.gz

```

## Sfle: expand anchors

* anchorLong

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

anchr cover \
    --parallel 16 \
    -c 2 -m 40 \
    -b 20 --len 1000 --idt 0.9 \
    merge/anchor.merge.fasta \
    canu-raw-40x/Sfle.trimmedReads.fasta.gz \
    -o merge/anchor.cover.fasta

rm -fr anchorLong
anchr overlap2 \
    --parallel 16 \
    merge/anchor.cover.fasta \
    canu-raw-40x/Sfle.trimmedReads.fasta.gz \
    -d anchorLong \
    -b 20 --len 1000 --idt 0.98

anchr overlap \
    merge/anchor.cover.fasta \
    --serial --len 10 --idt 0.9999 \
    -o stdout \
    | perl -nla -e '
        BEGIN {
            our %seen;
            our %count_of;
        }

        @F == 13 or next;
        $F[3] > 0.9999 or next;

        my $pair = join( "-", sort { $a <=> $b } ( $F[0], $F[1], ) );
        next if $seen{$pair};
        $seen{$pair} = $_;

        $count_of{ $F[0] }++;
        $count_of{ $F[1] }++;

        END {
            for my $pair ( keys %seen ) {
                my ($f_id, $g_id) = split "-", $pair;
                next if $count_of{$f_id} > 2;
                next if $count_of{$g_id} > 2;
                print $seen{$pair};
            }
        }
    ' \
    | sort -k 1n,1n -k 2n,2n \
    > anchorLong/anchor.ovlp.tsv

ANCHOR_COUNT=$(faops n50 -H -N 0 -C anchorLong/anchor.fasta)
echo ${ANCHOR_COUNT}

rm -fr anchorLong/group
anchr group \

doc/bacteria_2_3.md  view on Meta::CPAN

    | faops filter -a 1000 -l 0 stdin merge/anchor.merge.fasta

# merge others
anchr contained \
    Q20L60_2000000/anchor/pe.others.fa \
    Q25L60_2000000/anchor/pe.others.fa \
    Q30L60_2000000/anchor/pe.others.fa \
    --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

# 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 \
    1_genome/paralogs.fas \
    --label "merge,paralogs" \
    -o 9_qa

```

## Vpar: 3GS

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

canu \
    -p Vpar -d canu-raw-40x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=5.2m \
    -pacbio-raw 3_pacbio/pacbio.40x.fasta

canu \
    -p Vpar -d canu-raw-80x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=5.2m \
    -pacbio-raw 3_pacbio/pacbio.80x.fasta

faops n50 -S -C canu-raw-40x/Vpar.trimmedReads.fasta.gz
faops n50 -S -C canu-raw-80x/Vpar.trimmedReads.fasta.gz

```

## Vpar: expand anchors

* anchorLong

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

anchr cover \
    --parallel 16 \
    -c 2 -m 40 \
    -b 20 --len 1000 --idt 0.9 \
    merge/anchor.merge.fasta \
    canu-raw-40x/Vpar.trimmedReads.fasta.gz \
    -o merge/anchor.cover.fasta

rm -fr anchorLong
anchr overlap2 \
    --parallel 16 \
    merge/anchor.cover.fasta \
    canu-raw-40x/Vpar.trimmedReads.fasta.gz \
    -d anchorLong \
    -b 20 --len 1000 --idt 0.98

anchr overlap \
    merge/anchor.cover.fasta \
    --serial --len 10 --idt 0.9999 \
    -o stdout \
    | perl -nla -e '
        BEGIN {
            our %seen;
            our %count_of;
        }

        @F == 13 or next;
        $F[3] > 0.9999 or next;

        my $pair = join( "-", sort { $a <=> $b } ( $F[0], $F[1], ) );
        next if $seen{$pair};
        $seen{$pair} = $_;

        $count_of{ $F[0] }++;
        $count_of{ $F[1] }++;

        END {
            for my $pair ( keys %seen ) {
                my ($f_id, $g_id) = split "-", $pair;
                next if $count_of{$f_id} > 2;
                next if $count_of{$g_id} > 2;
                print $seen{$pair};
            }
        }
    ' \
    | sort -k 1n,1n -k 2n,2n \
    > anchorLong/anchor.ovlp.tsv

ANCHOR_COUNT=$(faops n50 -H -N 0 -C anchorLong/anchor.fasta)
echo ${ANCHOR_COUNT}

rm -fr anchorLong/group
anchr group \

doc/bacteria_2_3.md  view on Meta::CPAN

# merge others
anchr contained \
    Q20L60_2000000/anchor/pe.others.fa \
    Q25L60_2000000/anchor/pe.others.fa \
    Q30L60_2000000/anchor/pe.others.fa \
    --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

# 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

```

## Lpne: 3GS

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

canu \
    -p Lpne -d canu-raw-40x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=3.4m \
    -pacbio-raw 3_pacbio/pacbio.40x.fasta

canu \
    -p Lpne -d canu-raw-80x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=3.4m \
    -pacbio-raw 3_pacbio/pacbio.80x.fasta

faops n50 -S -C canu-raw-40x/Lpne.trimmedReads.fasta.gz
faops n50 -S -C canu-raw-80x/Lpne.trimmedReads.fasta.gz

```

## Lpne: expand anchors

* anchorLong

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

anchr cover \
    --parallel 16 \
    -c 2 -m 40 \
    -b 20 --len 1000 --idt 0.9 \
    merge/anchor.merge.fasta \
    canu-raw-40x/Lpne.trimmedReads.fasta.gz \
    -o merge/anchor.cover.fasta

rm -fr anchorLong
anchr overlap2 \
    --parallel 16 \
    merge/anchor.cover.fasta \
    canu-raw-40x/Lpne.trimmedReads.fasta.gz \
    -d anchorLong \
    -b 20 --len 1000 --idt 0.98

anchr overlap \
    merge/anchor.cover.fasta \
    --serial --len 10 --idt 0.9999 \
    -o stdout \
    | perl -nla -e '
        BEGIN {
            our %seen;
            our %count_of;
        }

        @F == 13 or next;
        $F[3] > 0.9999 or next;

        my $pair = join( "-", sort { $a <=> $b } ( $F[0], $F[1], ) );
        next if $seen{$pair};
        $seen{$pair} = $_;

        $count_of{ $F[0] }++;
        $count_of{ $F[1] }++;

        END {
            for my $pair ( keys %seen ) {
                my ($f_id, $g_id) = split "-", $pair;
                next if $count_of{$f_id} > 2;
                next if $count_of{$g_id} > 2;
                print $seen{$pair};
            }
        }
    ' \
    | sort -k 1n,1n -k 2n,2n \
    > anchorLong/anchor.ovlp.tsv

ANCHOR_COUNT=$(faops n50 -H -N 0 -C anchorLong/anchor.fasta)
echo ${ANCHOR_COUNT}

rm -fr anchorLong/group
anchr group \

doc/bacteria_2_3.md  view on Meta::CPAN

# merge others
anchr contained \
    Q20L60_2000000/anchor/pe.others.fa \
    Q25L60_2000000/anchor/pe.others.fa \
    Q30L60_2000000/anchor/pe.others.fa \
    --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

# 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

```

## Ngon: 3GS

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

canu \
    -p Ngon -d canu-raw-40x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=2.3m \
    -pacbio-raw 3_pacbio/pacbio.40x.fasta

canu \
    -p Ngon -d canu-raw-80x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=2.3m \
    -pacbio-raw 3_pacbio/pacbio.80x.fasta

faops n50 -S -C canu-raw-40x/Ngon.trimmedReads.fasta.gz
faops n50 -S -C canu-raw-80x/Ngon.trimmedReads.fasta.gz

```

## Ngon: expand anchors

* anchorLong

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

anchr cover \
    --parallel 16 \
    -c 2 -m 40 \
    -b 20 --len 1000 --idt 0.9 \
    merge/anchor.merge.fasta \
    canu-raw-40x/Ngon.trimmedReads.fasta.gz \
    -o merge/anchor.cover.fasta

rm -fr anchorLong
anchr overlap2 \
    --parallel 16 \
    merge/anchor.cover.fasta \
    canu-raw-40x/Ngon.trimmedReads.fasta.gz \
    -d anchorLong \
    -b 20 --len 1000 --idt 0.98

anchr overlap \
    merge/anchor.cover.fasta \
    --serial --len 10 --idt 0.9999 \
    -o stdout \
    | perl -nla -e '
        BEGIN {
            our %seen;
            our %count_of;
        }

        @F == 13 or next;
        $F[3] > 0.9999 or next;

        my $pair = join( "-", sort { $a <=> $b } ( $F[0], $F[1], ) );
        next if $seen{$pair};
        $seen{$pair} = $_;

        $count_of{ $F[0] }++;
        $count_of{ $F[1] }++;

        END {
            for my $pair ( keys %seen ) {
                my ($f_id, $g_id) = split "-", $pair;
                next if $count_of{$f_id} > 2;
                next if $count_of{$g_id} > 2;
                print $seen{$pair};
            }
        }
    ' \
    | sort -k 1n,1n -k 2n,2n \
    > anchorLong/anchor.ovlp.tsv

ANCHOR_COUNT=$(faops n50 -H -N 0 -C anchorLong/anchor.fasta)
echo ${ANCHOR_COUNT}

rm -fr anchorLong/group
anchr group \

doc/bacteria_2_3.md  view on Meta::CPAN

    $(
        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 ::: 000 001 002 003 004 005 006
    ) \
    --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

# anchors sorted 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

```

## Nmen: 3GS

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

canu \
    -p Nmen -d canu-raw-40x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=2.3m \
    -pacbio-raw 3_pacbio/pacbio.40x.fasta

canu \
    -p Nmen -d canu-raw-80x \
    gnuplot=$(brew --prefix)/Cellar/$(brew list --versions gnuplot | sed 's/ /\//')/bin/gnuplot \
    genomeSize=2.3m \
    -pacbio-raw 3_pacbio/pacbio.80x.fasta

faops n50 -S -C canu-raw-40x/Nmen.trimmedReads.fasta.gz
faops n50 -S -C canu-raw-80x/Nmen.trimmedReads.fasta.gz

```

## Nmen: expand anchors

* anchorLong

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

anchr cover \
    --parallel 16 \
    -c 2 -m 40 \
    -b 20 --len 1000 --idt 0.9 \
    merge/anchor.merge.fasta \
    canu-raw-40x/${BASE_NAME}.trimmedReads.fasta.gz \
    -o merge/anchor.cover.fasta

rm -fr anchorLong
anchr overlap2 \
    --parallel 16 \
    merge/anchor.cover.fasta \
    canu-raw-40x/${BASE_NAME}.trimmedReads.fasta.gz \
    -d anchorLong \
    -b 20 --len 1000 --idt 0.98

anchr overlap \
    merge/anchor.cover.fasta \
    --serial --len 10 --idt 0.9999 \
    -o stdout \
    | perl -nla -e '
        BEGIN {
            our %seen;
            our %count_of;
        }

        @F == 13 or next;
        $F[3] > 0.9999 or next;

        my $pair = join( "-", sort { $a <=> $b } ( $F[0], $F[1], ) );
        next if $seen{$pair};
        $seen{$pair} = $_;

        $count_of{ $F[0] }++;
        $count_of{ $F[1] }++;

        END {
            for my $pair ( keys %seen ) {
                my ($f_id, $g_id) = split "-", $pair;
                next if $count_of{$f_id} > 2;
                next if $count_of{$g_id} > 2;
                print $seen{$pair};
            }
        }
    ' \
    | sort -k 1n,1n -k 2n,2n \
    > anchorLong/anchor.ovlp.tsv

ANCHOR_COUNT=$(faops n50 -H -N 0 -C anchorLong/anchor.fasta)
echo ${ANCHOR_COUNT}

rm -fr anchorLong/group
anchr group \

doc/bacteria_2_3.md  view on Meta::CPAN

        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 80 120 160 240 ::: 000 001 002 003 004 005 006
    ) \
    --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

# anchors sorted 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

```

## Cdip: 3GS

```bash
BASE_NAME=Cdip
REAL_G=2488635
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

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

```

## Cdip: expand anchors

* anchorLong

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

anchr cover \
    --parallel 16 \
    -c 2 -m 40 \
    -b 20 --len 1000 --idt 0.9 \
    merge/anchor.merge.fasta \
    canu-raw-40x/${BASE_NAME}.trimmedReads.fasta.gz \
    -o merge/anchor.cover.fasta

rm -fr anchorLong
anchr overlap2 \
    --parallel 16 \
    merge/anchor.cover.fasta \
    canu-raw-40x/${BASE_NAME}.trimmedReads.fasta.gz \
    -d anchorLong \
    -b 20 --len 1000 --idt 0.98

anchr overlap \
    merge/anchor.cover.fasta \
    --serial --len 10 --idt 0.9999 \
    -o stdout \
    | perl -nla -e '
        BEGIN {
            our %seen;
            our %count_of;
        }

        @F == 13 or next;
        $F[3] > 0.9999 or next;

        my $pair = join( "-", sort { $a <=> $b } ( $F[0], $F[1], ) );
        next if $seen{$pair};
        $seen{$pair} = $_;

        $count_of{ $F[0] }++;
        $count_of{ $F[1] }++;

        END {
            for my $pair ( keys %seen ) {
                my ($f_id, $g_id) = split "-", $pair;
                next if $count_of{$f_id} > 2;
                next if $count_of{$g_id} > 2;
                print $seen{$pair};
            }
        }
    ' \
    | sort -k 1n,1n -k 2n,2n \
    > anchorLong/anchor.ovlp.tsv

ANCHOR_COUNT=$(faops n50 -H -N 0 -C anchorLong/anchor.fasta)
echo ${ANCHOR_COUNT}

rm -fr anchorLong/group
anchr group \

doc/bacteria_2_3.md  view on Meta::CPAN

        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 ::: 000 001 002 003 004 005 006
    ) \
    --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

# anchors sorted 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

```

## Ftul: 3GS

```bash
BASE_NAME=Ftul
GENOME_SIZE=1.9m
cd $HOME/data/anchr/${BASE_NAME}

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

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

```

## Ftul: expand anchors

* anchorLong

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

anchr cover \
    --parallel 16 \
    -c 2 -m 40 \
    -b 20 --len 1000 --idt 0.9 \
    merge/anchor.merge.fasta \
    canu-raw-40x/${BASE_NAME}.trimmedReads.fasta.gz \
    -o merge/anchor.cover.fasta

rm -fr anchorLong
anchr overlap2 \
    --parallel 16 \
    merge/anchor.cover.fasta \
    canu-raw-40x/${BASE_NAME}.trimmedReads.fasta.gz \
    -d anchorLong \
    -b 20 --len 1000 --idt 0.98

anchr overlap \
    merge/anchor.cover.fasta \
    --serial --len 10 --idt 0.9999 \
    -o stdout \
    | perl -nla -e '
        BEGIN {
            our %seen;
            our %count_of;
        }

        @F == 13 or next;
        $F[3] > 0.9999 or next;

        my $pair = join( "-", sort { $a <=> $b } ( $F[0], $F[1], ) );
        next if $seen{$pair};
        $seen{$pair} = $_;

        $count_of{ $F[0] }++;
        $count_of{ $F[1] }++;

        END {
            for my $pair ( keys %seen ) {
                my ($f_id, $g_id) = split "-", $pair;
                next if $count_of{$f_id} > 2;
                next if $count_of{$g_id} > 2;
                print $seen{$pair};
            }
        }
    ' \
    | sort -k 1n,1n -k 2n,2n \
    > anchorLong/anchor.ovlp.tsv

ANCHOR_COUNT=$(faops n50 -H -N 0 -C anchorLong/anchor.fasta)
echo ${ANCHOR_COUNT}

rm -fr anchorLong/group
anchr group \