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
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]
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] --pairs-to-stdout Write the paired reads to stdout --all-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] --aligned --no-aligned Reads in the BAM that are aligned will (will not) be extracted. [Default: extract aligned reads] --unaligned --no-unaligned Reads in the BAM that are not aligned will (will not) be extracted. [Default: extract unaligned reads] --filtered --no-filtered 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]
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.