Results for "FM-index"
Bio-Scripts
#!/usr/bin/perl # make three strings of nucleotides $dna1 = “AAAAAAAAAAAAAAATGAAAAAAAAAAAAAAAA”; $dna2 = “AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA”; $dna3 = “ATGAAAAA...2924 days ago
Perl script introduces control structures, arrays and hashes.
#!/usr/bin/env perl use strict; use warnings; my @first_array = ('DNA', 'ATGCGTGC', 5, 'RNA', 'AUGC'); print $first_array[0], "\n\n"; # Scalar gives actual si...2877 days ago
Blast script to index and extract sequence !!
# look at the file $ head EC4115.fa >NC_011353.1 Escherichia coli O157:H7 str. EC4115 chromosome, complete genome. AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAA...2867 days ago
Install ATOM editor on Elemantory OS / Ubuntu
#Download ATOM deb file from https://atom.io/ https://atom.io/download/deb (base) bioqueen@bioqueen-Lenovo-ideapad-320-15ISK:~/Downloads/$ sudo apt install ./atom-am...1191 days ago
Genetic Algorithms demonstration with word DNA in Perl
#!/usr/bin/perl -w # GA demonstration with word DNA (512 bits) use strict; use Data::Dumper; # individuals in the population my $popsize = 1024; # a good st...2387 days ago
Bash script to convert SAM to BAM visualization ready
samtools view -bS file.sam | samtools sort - file_sorted samtools index test_sorted.bam test_sorted.bai2198 days ago
Perl script to convert GFF 2 FASTA !
#!/usr/bin/perl use strict; use warnings; use Bio::Seq; use Bio::SeqIO; use Bio::DB::Fasta; $| = 1; # Flush output my $outfile_cds = Bio::SeqIO->new( -format...2154 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 is a bash scrip to map your long reads and make it v...2137 days ago
- ➜ Tools git:(master) ✗ git clone https://github.com/Nextomics/nextsv.git Cloning into 'nextsv'... remote: Counting objects: 369, done. remote: Total 369 (delta 0),...
2113 days ago
- jitendra@jitendra-UNLOCK-INSTALL[SNP] wget https://github.com/broadinstitute/gatk/releases/download/4.0.2.1/gatk-4.0.2.1.zip --2018-08-30 11:47:20-- https://github.com...
2090 days ago
