Installing Busco version 4.0.6
(base) jit@jit-HP-Pro-3335-MT: conda install...environment location: /home/jit/anaconda3 added / update...12 KB conda-forge r-magrittr-1.5 | r36h6115d...B conda-forge r-prettyunits-1.1.1 | r36h6115d3...inux-64::perl-module-load-conditional-0.68-pl526_2 perl-mod...1512 days ago
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Perl script to extract a sequence from multifasta with range !
...arameter not provided\n"; { local $/=">"; while() { chomp; next unless /\w/; s/>$//gs; my @chunk = split /\n/; my $header = s...2125 days ago
Perl script to break the contigs by 'N'
...e NNNNN region in the contig my @regions=(); my @bases=split //,$seq; push(@bases,"E"); #This extra position marks the end of the conti...print "$lastregion $#regions\n"; die; my ($ini,$end)= split /\s+/,$lastregion; if (($e...2121 days ago
2119 days ago
Generates a genome coverage plot with R
library(CoverageView) ##draw a coverage plot for a test case BAM file #get a BAM test file treatBAMfile2114 days ago
Perl script to split fasta sequence / overlaps
#!/usr/bin/perl use strict; use warnings; my $len = 5000; my $over = 200; my $seq_id=$ARGV[0]; my $seqFile = $ARGV[1]; my $seq; open(my $fh, "2102 days ago
Perl script to reverse complement a DNA sequence !
...ent DNA: WRONG:\n\n"; print "$revcom\n"; print "\nThat was a bad algorithm, and the reverse complement...reverse complement DNA:\n\n"; print "$revcom\n"; print "\nThis time it worked!\n\n"; exit;2102 days ago
Installing pb-assembly on Linux !
...METIS/5.1.0-foss-2016a-32bitIDX Coreutils/8.22-goolf-1.4....PROJ/4.8.0-goolf-1.4.10 git/2.2.2...bioconda libedit: 3.1.20170329-haf1bff...py27_1001 conda-forge sqlite 3.25.2...2093 days ago