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
Tools need to be loaded by conda (with some exceptions). 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.