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Bash script to simulate a genome !
By Abhinav 911 days ago
# Reference https://github.com/chhylp123/hifiasm/issues/33
# Use Drosophila melongaster PacBio assembly
cd /genetics/elbers/test/fly2
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/401/745/GCA_003401745.1_ASM340174v1/GCA_003401745.1_ASM340174v1_genomic.fna.gz
# Use BCFtools 1.10.2 and SAMtools 1.10
conda activate bcftools1.10.2
# Use Seqtk to convert soft-masked bases to upper-case bases, also compress with bgzip
# https://github.com/lh3/seqtk
/genetics/elbers/bin/seqtk/seqtk seq -U \
GCA_003401745.1_ASM340174v1_genomic.fna.gz | \
bgzip -@75 > GCA_003401745.1_ASM340174v1_genomic.fna_upper.fasta.gz
# Convert to diploid with approximately 2% heterozygosity rate, max indels=20bp
# mutate.sh part of BBTools/BBMap https://sourceforge.net/projects/bbmap/
/genetics/elbers/bbmap-38.86/mutate.sh \
in=GCA_003401745.1_ASM340174v1_genomic.fna_upper.fasta.gz \
ow=t \
vcf=GCA_003401745.1_ASM340174v1_genomic.fna_upper.diploid.vcf.gz \
out=GCA_003401745.1_ASM340174v1_genomic.fna_upper.diploid.fasta.gz \
ziplevel=6 \
ploidy=2 \
subrate=0.0192 \
indelrate=0.001 \
maxindel=20 \
nohomopolymers=t \
hetrate=1 2> GCA_003401745.1_ASM340174v1_genomic.fna_upper.diploid.fasta.log.txt
# genome size
bgzip -@75 -cd GCA_003401745.1_ASM340174v1_genomic.fna_upper.fasta.gz | \
grep -v ">"|wc -m
# 140687135
# 2% heterozygosity is how many bases
calc 0.02\*140687135
# 0.02*140687135 = 2813742.700000
# number of mutations added
bgzip -@75 -cd GCA_003401745.1_ASM340174v1_genomic.fna_upper.diploid.vcf.gz| \
grep -v "^#"|wc -l
# 2830139
# ~2% het rate
# get only 1 haplotype from the "diploid" reference
bgzip -@75 -dc GCA_003401745.1_ASM340174v1_genomic.fna_upper.diploid.fasta.gz|\
/genetics/elbers/bin/seqtk/seqtk seq -L0|paste - - |grep -P "haplo_0\t"| \
tr '\t' '\n' |\
/genetics/elbers/bin/seqtk/seqtk seq -L60 |\
bgzip -@75 \
> GCA_003401745.1_ASM340174v1_genomic.fna_upper.diploid.haplotype0.fasta.gz
# make reference for randomreads.sh
# randomreads.sh part of BBTools/BBMap https://sourceforge.net/projects/bbmap/
/genetics/elbers/bbmap-38.86/randomreads.sh build=1 \
seed=1 \
ref=GCA_003401745.1_ASM340174v1_genomic.fna_upper.diploid.fasta.gz \
illuminanames=t addslash=t \
pacbio=t pbmin=0.13 pbmax=0.17 \
reads=100 paired=f \
gaussianlength=t \
minlength=1000 midlength=20000 maxlength=100000 \
out=/dev/null
# make 60x haploid coverage for Illumina reads
/genetics/elbers/bbmap-38.86/randomreads.sh build=1 \
ref=GCA_003401745.1_ASM340174v1_genomic.fna_upper.diploid.fasta.gz \
illuminanames=t addslash=t \
coverage=30 paired=t maxinsert=550 mininsert=450 \
out1=illumina1.fastq.gz out2=illumina2.fastq.gz > random_reads_illumina.log 2>&1
# interleave the paired-end reads
# reformat.sh part of BBTools/BBMap https://sourceforge.net/projects/bbmap/
/genetics/elbers/bbmap-38.86/reformat.sh \
in=illumina1.fastq.gz in2=illumina2.fastq.gz out=illumina.int.fastq 2>/dev/null
# use KmerGenie 1.7051 to get an idea of k-mer with that produces longest N50
# http://kmergenie.bx.psu.edu/
mkdir -p /genetics/elbers/test/fly2/kmergenie-illumina-raw-reads
cd /genetics/elbers/test/fly2/kmergenie-illumina-raw-reads
/genetics/elbers/kmergenie-1.7051/kmergenie ../illumina.int.fastq \
> kmergenie-illumina-raw-reads.log 2>&1
rm ../illumina.int.fastq
k=`grep "^best k:" \
kmergenie-illumina-raw-reads.log | grep -Po "\d+"`
echo "best k=${k}"
# make 30x haploid coverage for PacBio CLR reads
# error rate from 13 - 15 % minimum 1000bp midlength 20000bp maximum 30000bp
cd /genetics/elbers/test/fly2
/genetics/elbers/bbmap-38.86/randomreads.sh build=1 \
ow=t seed=1 \
ref=GCA_003401745.1_ASM340174v1_genomic.fna_upper.diploid.fasta.gz \
illuminanames=t addslash=t \
pacbio=t pbmin=0.13 pbmax=0.15 \
coverage=15 paired=f \
gaussianlength=t \
minlength=1000 midlength=20000 maxlength=30000 \
out=pacbio.fastq.gz > random_reads_pacbio.log 2>&1
# make 30x haploid coverage for PacBio reads for Hifi reads
# error rate from 1 - 0.1 % minimum 9000bp midlength 10000bp max 12000bp
/genetics/elbers/bbmap-38.86/randomreads.sh build=1 \
ow=t seed=1 \
ref=GCA_003401745.1_ASM340174v1_genomic.fna_upper.diploid.fasta.gz \
illuminanames=t addslash=t \
pacbio=t pbmin=0.001 pbmax=0.01 \
coverage=15 paired=f \
gaussianlength=t \
minlength=9000 midlength=10000 maxlength=12000 \
out=hifi.fastq.gz > random_reads_pacbio_hifi.log 2>&1
