Tools

All you have to know about the command line tools Migale provide

Description

Many tools are available on the Migale facility.They are open-source bioinformatics software made for linux platform. You can access them via the command line on the front server.

List of available tools

conda info --envs #Show all conda environments

Conda environment

Tools need to be loaded by conda (with some exceptions). See the FAQ for details on how to use conda.

• Example with bwa:

[stage01@front ~]$ conda activate bwa-0.7.17
(bwa-0.7.17) [stage01@front ~]$ bwa

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.17-r1188
Contact: Heng Li 

Usage:   bwa command  [options]

Command: index         index sequences in the FASTA format
         mem           BWA-MEM algorithm
         fastmap       identify super-maximal exact matches
         pemerge       merge overlapping paired ends (EXPERIMENTAL)
         aln           gapped/ungapped alignment
         samse         generate alignment (single ended)
         sampe         generate alignment (paired ended)
         bwasw         BWA-SW for long queries

         shm           manage indices in shared memory
         fa2pac        convert FASTA to PAC format
         pac2bwt       generate BWT from PAC
         pac2bwtgen    alternative algorithm for generating BWT
         bwtupdate     update .bwt to the new format
         bwt2sa        generate SA from BWT and Occ

Note: To use BWA, you need to first index the genome with `bwa index'.
      There are three alignment algorithms in BWA: `mem', `bwasw', and
      `aln/samse/sampe'. If you are not sure which to use, try `bwa mem'
      first. Please `man ./bwa.1' for the manual