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 migale server or via the Galaxy portal.

List of available tools

Default installation

Some tools are set in the $PATH environment variable, you can access them by entering their names.

Example with bam2fastq
[stage01@migale ~]$ bam2fastq
bam2fastq v1.1.0 - extract sequences from a BAM file

Usage: bam2fastq [options] 

  -o FILENAME, --output FILENAME
       Specifies the name of the FASTQ file(s) that will be generated.  May
       contain the special characters % (replaced with the lane number) and
       # (replaced with _1 or _2 to distinguish PE reads, _M for unpaired reads).
       [Default: s_%#_sequence.txt]

       Write the paired reads to stdout 

       Write all reads to stdout, ignoring pairing

  -f, --force, --overwrite
       Create output files specified with --output, overwriting existing
       files if necessary [Default: exit program rather than overwrite files]

       Reads in the BAM that are aligned will (will not) be extracted.
       [Default: extract aligned reads]

       Reads in the BAM that are not aligned will (will not) be extracted.
       [Default: extract unaligned reads]

       Reads that are marked as failing QC checks will (will not) be extracted.
       [Default: extract filtered reads]

  -q, --quiet
       Suppress informational messages [Default: print messages]

  -s, --strict
       Keep bam2fastq's processing to a minimum, assuming that the BAM strictly       meets specifications. [Default: allow some errors in the BAM]

Conda environment

Some tools need to be loaded by conda. See the FAQ for details on how to use conda.

Example with bwa
[stage01@migale ~]$ conda activate bwa-0.7.17
(bwa-0.7.17) [stage01@migale ~]$ 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.