SPAdes St. Petersburg genome assembler is intended for both standard isolate and single-cell MDA bacteria assemblies.

References:

• If you use SPAdes in your research, please include Nurk, Bankevich et al., 2013 in your reference list. You can also add Bankevich, Nurk et al., 2012 instead.

• http://spades.bioinf.spbau.ru/release3.6.1/manual.html#sec4

• Module Name: spades (see the modules page for more information)
• Multithreaded
• Example files in /usr/local/apps/spades/3.11.0/share/spades/

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=4
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load spades
[user@cn3144 ~]$ spades.py -t $SLURM_CPUS_PER_TASK -o outfile -1 infile_1.fq.gz -2 infile_2.fq.gz
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. spades.sh). For example:

#!/bin/bash
set -e
module load spades
spades.py -t $SLURM_CPUS_PER_TASK -o outfile -1 infile_1.fq.gz -2 infile_2.fq.gz

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 spades.sh

Create a swarmfile (e.g. spades.swarm). For example:

cd dir1; spades.py -t $SLURM_CPUS_PER_TASK -o outfile -1 infile_1.fq.gz -2 infile_2.fq.gz
cd dir2; spades.py -t $SLURM_CPUS_PER_TASK -o outfile -1 infile_1.fq.gz -2 infile_2.fq.gz
cd dir3; spades.py -t $SLURM_CPUS_PER_TASK -o outfile -1 infile_1.fq.gz -2 infile_2.fq.gz

Submit this job using the swarm command.

swarm -f spades.swarm -t 4 --module spades