Insert the sequence at desire location in multi-fasta file with Perl
#!/usr/bin/perl use warnings; use strict; use Bio::SeqIO; use Bio::Seq; use File::Copy; #ARGV[0] should be in following format --- Keep the coordinate sorted...2354 days ago
Create genome scaffolding with Perl
#!/usr/bin/perl use warnings; use strict; use English; use Pod::Usage; ## uses pod documentation in usage code use Getopt::Long qw(:config auto_version auto_h...2348 days ago
890 days ago
Perl script to remove fasta sequences in multifasta file with certain length threshold
#!/usr/bin/perl use strict; use warnings; my $minlen = shift or die "Error: `minlen` parameter not provided\n"; { local $/=">"; while() { cho...2291 days ago
Perl script to convert fastq to fasta file
#!/usr/bin/env perl use strict; use warnings; use Bio::Factory::EMBOSS; my $usa...=> 'fastq', -outseq => $outfile, -osformat => 'fasta'});2291 days ago
Perl script to read multi fasta sequence one by one
...anRun.pl seq.fa my $outfile='tmp.fa'; my $fastaSeq_ref = readfasta ("$ARGV[0]"); my %fastaSeq =...n the file $outfile $!"; print OUT "$key\n$fastaSeq{$key}\n"; } sub re...emp_seq; #suppose fasta files contains multiple sequences; open (IN,...2261 days ago
2250 days ago
Perl script to find coding regions in DNA sequences
#!/usr/bin/perl -w use strict; # if the number of input arguments is lower than...naloglkh.pl: the file $filesequence can not be opened\n"; exit(1); } # FASTA format: # >header containin...2195 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
BAM files and mapping BESST requires sorted and indexed BAM files as input. Any read a...hon reads_to_ctg_map.py /path/to/lib1_A.fq /path/to/lib1_B.fq /path/to/contigs.fasta --threads N where N is an in...2164 days ago
Perl script to count number of Ns in a multifasta file !
#!/usr/bin/perl my ($h, $n, $l); open(I,$ARGV[0]) or die($!); while(){ cho...ces in oneline first perl -pe '/^>/ ? print "\n" : chomp' scaffolds_backup.fasta > out.fasta perl countN.pl scaff.fa...2184 days ago