Perl script to break the contigs by 'N'
#!/usr/bin/perl -w use Bio::SeqIO; use strict; my $fasta = Bio::SeqIO->new( -file => "$ARGV[0].parts.fasta",-format=>'fasta'); open(SCAFF,">$ARGV[0].parts.scaff"...2065 days ago
Generate simulated polyploid genome !
#Generate 3% divergence msbar -point 4 -count 16558 toy.fasta > toyheterozygous3percent.fasta #Cat both files cat toy.fasta toymutated3percent.fasta > toyheterozy...2055 days ago
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Samtools commands for bioinformatician !
## count mapped reads samtools view -c -F 260 mapping_file.bam ### converting sam file into fasta samtools fasta reads_mapped.sam > reads.fasta ### converting...1605 days ago
Bash script to download SRA file !
#We can use the sratoolkit to directly pull the sequence data (in paired FASTQ format) from the archive. fastq-dump is in the SRA toolkit. It allows directly downloading...1561 days ago
Bash commandline to install Anaconda !
#The line begins with $ are the commands $ mkdir tmp $ cd tmp/ $ curl -O https://repo.anaconda.com/archive/Anaconda3-2019.03-Linux-x86_64.sh % Total % Re...1558 days ago
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