Perl script to merge LastZ overlaps
#!/usr/bin/perl use strict; use warnings; use 5.010; # Filter out the exact/direct overlaps from tab seperated alignment file. (lastz format=general- ready) # Do not inclide header in lastz outfile # USAGE: perl filterOverlaps.pl infile > outfile open my $fh, '2139 days ago
Long reads mapper bash script !
#!/bin/bash #only for LONG READS mapping #USAGE: runMapper.sh minima...ready !" #Location of the tools samtools=/home/urbe/anaconda3/bin/samtools graphMapLoc=/home/urbe/Tools/graphmap/bin/Linux-x64/graphmap minimap2L...2136 days ago
Installing Porechop on Ubuntu !
...ning install_scripts Installing porechop script to /home/urbe/anaconda3/bin ➜ Porechop git:(master) por...or adapter alignment (default: 16) Barcode binning settings: Control the...2120 days ago
2113 days ago
Perl script to find palindromic pattern !
#!/usr/bin/perl use strict; use warnings; use strict; my %invert; @invert{ qw[ A C G T ] } = qw[ T G C A ]; my $in = do{ local $/; }; chomp $in; print $in; for m...2113 days ago
2112 days ago
Install Python locally on shared Linux server !
...his command: which python #it should show you the path to the python binary file, which is located in....bashrc_profile and add the #following line: export PATH=$HOME/.local/bin:$PATH #Again, reload the ses...2112 days ago
Perl script to extract sequence by Ids from multifasta file !
#!/usr/bin/perl -w use strict; my $idsfile = "$ARGV[0]"; my $seqfile = "$ARGV[1]"; my %ids = (); open FILE, $idsfile; while() { chomp; $ids{$_} += 1;...2110 days ago
Perl script to extract a sequence from multifasta with range !
# filterfastarange.pl #!/usr/bin/perl use strict; use warnings; #perl filterfastarange.pl 301 600 contigs.fasta > contigs-gt300-lte600.fasta my $minlen = shift or die "Erro...2080 days ago
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")...2077 days ago