metaSPAdes Assembly

SPAdes – St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines. See the SPAdes home page for more info.

metaSPAdes can be run by the following command:

cd /vol/spool/workdir/assembly/

qsub -cwd -pe multislot 14 -N metaspades -b y \
/usr/local/lib/SPAdes-3.11.1-Linux/bin/metaspades.py -o metaspades_out --pe1-1 read1.fq --pe1-2 read2.fq

The contig sequences are located in the metaspades_out directory in file contigs.fasta. Again, let’s get some basic statistics on the contigs:

getN50.pl -s 500 -f metaspades_out/contigs.fasta

Note

Most jobs above will be started on the compute cluster using the qsub.

  • qstat: check the status and JOBNUMBER of your jobs
  • qdel JOBNUMBER: delete job with job number JOBNUMBER

We usually submit the jobs to the cluster giving them a job name by using -N JOBNAME. This will create log-files named

  • JOBNAME.oJOBNUMBER: standard output messages of the tool
  • JOBNAME.eJOBNUMBER: standard error messages of the tool

You can look into these files by typing e.g. less JOBNAME.oJOBNUMBER (hit q to quit) or tail -f JOBNAME.oJOBNUMBER (hit ^C to quit).