SPAdes – St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines.1
The following versions are installed and currently available...
... on environment hpc-env/8.3:
Loading / Using SPAdes
To load the desired version of the module, use the module load command, e.g.
module load hpc-env/8.3 module load SPAdes
Always remember: this command is case sensitive!
SPAdes contains multiple executables and scripts which you can print out after loading the module with the command: ls -l $EBROOTSPADES/bin
Some executables provide additional help instructions. E.g. for spades-bwa you can call the executable spades-bwa without arguments to print out a help text to get you started:
$ spades-bwa Program: bwa (alignment via Burrows-Wheeler transformation) Version: 0.7.16a-r1181 Contact: Heng Li <firstname.lastname@example.org> 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 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.
The full documentation can be found here.