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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.


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:

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