High-Performance Computing at the NIH
GitHub YouTube @nih_hpc RSS Feed
SPINGO

SPINGO (SPecies level IdentificatioN of metaGenOmic amplicons) is a flexible and stand-alone software dedicated to high-resolution assignment of sequences to species level using partial 16S rRNA gene sequences from any environment.

References:

There are multiple versions of SPINGO available. An easy way of selecting the version is to use modules. To see the modules available, type

module avail SPINGO

To select a module, type

module load SPINGO/[ver]

where [ver] is the version of choice.

Environment variables set:

Interactive job

Sample session:

module load SPINGO
spingo -d $SPINGODB/RDP_11.5.species.fa -i repr_set_seqs.fasta > spingo.out
Batch job on Biowulf

Create a batch input file (e.g. spingo.sh), which uses the input file 'my_amplicon.fa'. For example:

#!/bin/bash
module load SPINGO
spingo -d $SPINGODB/RDP_11.5.species.fa -i my_amplicon.fa > spingo.out

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=1 spingo.sh
Swarm of Jobs on Biowulf

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

spingo -d $SPINGODB/RDP_11.5.species.fa -i reads1.fa > spingo1.out
spingo -d $SPINGODB/RDP_11.5.species.fa -i reads2.fa > spingo2.out
spingo -d $SPINGODB/RDP_11.5.species.fa -i reads3.fa > spingo3.out
spingo -d $SPINGODB/RDP_11.5.species.fa -i reads4.fa > spingo4.out

Submit this job using the swarm command.

swarm -f spingo.swarm --module SPINGO
Documentation