App-Anchr
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doc/model_organisms.md view on Meta::CPAN
## 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 \
doc/model_organisms.md view on Meta::CPAN
cat stat2.md
```
| Name | SumCor | CovCor | N50SR | Sum | # | N50Anchor | Sum | # | N50Others | Sum | # | Kmer | RunTimeKU | RunTimeAN |
|:--------------|-------:|-------:|------:|--------:|------:|----------:|--------:|------:|----------:|------:|-----:|--------------------------:|----------:|:----------|
| Q25L60X40P000 | 5.5G | 40.0 | 15071 | 120.4M | 17971 | 15570 | 115.59M | 13374 | 895 | 4.81M | 4597 | "31,41,43,45,51,61,71,81" | 1:49'30'' | 0:15'43'' |
| Q25L60X40P001 | 5.5G | 40.0 | 15022 | 120.25M | 18206 | 15611 | 115.64M | 13570 | 867 | 4.61M | 4636 | "31,41,43,45,51,61,71,81" | 1:51'20'' | 0:13'54'' |
| Q25L60X80P000 | 11.01G | 80.0 | 11442 | 120.49M | 21157 | 11891 | 115.59M | 16183 | 872 | 4.9M | 4974 | "31,41,43,45,51,61,71,81" | 2:29'52'' | 0:18'07'' |
| Q30L60X40P000 | 5.5G | 40.0 | 14735 | 120.17M | 18849 | 15237 | 115.12M | 13892 | 878 | 5.05M | 4957 | "31,41,43,45,51,61,71,81" | 1:50'40'' | 0:10'07'' |
| Q30L60X40P001 | 5.5G | 40.0 | 14182 | 120.1M | 19483 | 14723 | 114.97M | 14333 | 865 | 5.14M | 5150 | "31,41,43,45,51,61,71,81" | 1:50'22'' | 0:11'26'' |
| 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 \
doc/model_organisms.md view on Meta::CPAN
" ::: 25 30 ::: 60 ::: 30 60 ::: 000 001 002 003 004 005 006 \
>> stat2.md
cat stat2.md
```
| Name | SumCor | CovCor | N50SR | Sum | # | N50Anchor | Sum | # | N50Others | Sum | # | Kmer | RunTimeKU | RunTimeAN |
|:--------------|-------:|-------:|------:|-------:|------:|----------:|-------:|------:|----------:|-------:|-----:|--------------------:|----------:|:----------|
| Q25L60X30P000 | 3.01G | 30.0 | 10992 | 98.21M | 22237 | 11789 | 85.96M | 13658 | 2311 | 12.25M | 8579 | "31,41,51,61,71,81" | 1:14'53'' | 0:07'05'' |
| Q25L60X30P001 | 3.01G | 30.0 | 10433 | 97.91M | 23035 | 11351 | 85.44M | 13871 | 1562 | 12.47M | 9164 | "31,41,51,61,71,81" | 1:11'02'' | 0:07'05'' |
| 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
```
doc/model_organisms.md view on Meta::CPAN
| Name | SumCor | CovCor | N50SR | Sum | # | N50Anchor | Sum | # | N50Others | Sum | # | Kmer | RunTimeKU | RunTimeAN |
|:--------------|-------:|-------:|------:|--------:|------:|----------:|--------:|------:|----------:|------:|-----:|--------------------:|----------:|:----------|
| Q25L60X30P000 | 3.59G | 30.0 | 18855 | 111.65M | 15804 | 19553 | 107.56M | 10704 | 772 | 4.09M | 5100 | "31,41,51,61,71,81" | 0:45'55'' | 0:08'21'' |
| Q25L60X30P001 | 3.59G | 30.0 | 18866 | 111.54M | 15737 | 19640 | 107.63M | 10662 | 756 | 3.91M | 5075 | "31,41,51,61,71,81" | 0:47'00'' | 0:08'04'' |
| Q25L60X60P000 | 7.18G | 60.0 | 14905 | 112M | 18291 | 15590 | 107.37M | 12497 | 774 | 4.63M | 5794 | "31,41,51,61,71,81" | 1:15'44'' | 0:09'01'' |
| Q30L60X30P000 | 3.59G | 30.0 | 21148 | 111.75M | 15024 | 21979 | 107.66M | 9980 | 782 | 4.09M | 5044 | "31,41,51,61,71,81" | 0:46'32'' | 0:07'02'' |
| Q30L60X30P001 | 3.59G | 30.0 | 21449 | 111.75M | 14927 | 22226 | 107.69M | 9894 | 784 | 4.06M | 5033 | "31,41,51,61,71,81" | 0:43'51'' | 0:07'02'' |
| Q30L60X60P000 | 7.18G | 60.0 | 20909 | 112.14M | 15517 | 21888 | 107.76M | 10108 | 781 | 4.38M | 5409 | "31,41,51,61,71,81" | 1:14'33'' | 0:08'12'' |
## col_0: merge anchors
```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}
( run in 1.226 second using v1.01-cache-2.11-cpan-788537b7465 )