Long reads mapper bash script !
...2 ref.fa reads.fa/fq 48 ont echo -e "This is a bash scrip to map your long reads and...bin/ngmlr-0.2.3/ngmlr lamsaLoc=/home/urbe/Tools/LAMSA/lamsa...with $toolName" $bwaMemLoc index $refFasta $bwaMemLo...= "ont" ]; then $ngmlrLoc -t $thread -r $refFasta -q $l...2174 days ago
Perl subroutine to read genome/reads fasta file !
...ile = $_[0]; my (%map,$id,$seq); open(IN,$file) or die("Cannot open file for reading $file:$!\n"); while(){ chomp; if($_ =~ /^>/){ i...else { $seq=$seq.$_; } } $map{$id} = $seq; close(IN); return \%map; }...2185 days ago
2179 days ago
2178 days ago
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, '2177 days ago
2175 days ago
1568 days ago
Installing Porechop on Ubuntu !
➜ Tools git:(master) ✗ git clone https://github.com/rrwick/Porechop.git Cloning into 'Porechop'... remote: Counting obje...ckages/porechop/misc.py to misc.cpython-36.pyc byte-compilin...(default: 16) Barcode binning settings: Contr...2158 days ago
2151 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 $/; }; chomp...$pals, ($pals+1)*2 ), $p1-$pals; } } __DATA__ AGAGGTCAGTCTGCATCGTATCGATCGTCGACGATCG...2151 days ago