2915 days ago
2308 days ago
Perl script to check fastq reads qualities !
#!/usr/bin/env perl use strict; use warnings; sub readfq { my ($fh, $aux) = @_; @$aux = [undef, 0] if (!defined(@$aux)); return if ($aux->[1]); if (!def...2198 days ago
2253 days ago
Perl subroutine to read genome/reads fasta file !
sub readSeqFromFasta{ my $file = $_[0]; my (%map,$id,$seq); open(IN,$file) or die("Cannot open file for reading $file:$!\n"); while(){ chomp; if($_ =~ /^>/...2177 days ago
2171 days ago
2170 days ago
Long reads mapper bash script !
#!/bin/bash #only for LONG READS mapping #USAGE: runMapper.sh minimap2 ref.fa reads.fa/fq 48 ont echo -e "This i...$bwaMemLoc mem $refFasta $longReads -t $thread > $fileName.out.sa...pping with $toolName" if [ $readsType == "ont" ]; then $n...2166 days ago
2167 days ago
Installing Porechop on Ubuntu !
...stq.gz}] [-v VERBOSITY] [-t THREADS] [-b BARCODE_DIR]...d ADAPTER_THRESHOLD] [--check_reads CHECK_READS] [--scoring_schem...adapters found at the ends of reads (default: 2) --end_thresho...2150 days ago