SPAdes 2016

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SPAdes – St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines.1

Installed version(s)

The following versions are installed and currently available...

... on environment hpc-env/8.3:

  • SPAdes/3.15.3-GCC-8.3.0-Python-3.7.4
  • SPAdes/3.15.3-GCCcore-8.3.0-Python-3.7.4

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 <>

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.