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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

inStrain

inStrain is a Python program for the analysis of co-occurring genome populations from metagenomes. It performs strain-level comparisons, microdiversity analysis and non-synonymous variant identification from read mappings.

License

Free to use and open source under the MIT License.

Available

  • Roihu: 1.6.3 (module py-instrain), via the bio-apps module.

Usage

inStrain is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the module:

module load bio-apps/v202603
module load py-instrain/1.6.3

Profile a metagenomic mapping (a sorted BAM against a genome or set of genomes):

inStrain profile aligned.sorted.bam genomes.fasta -o instrain_out -p 8

Example batch script

#!/bin/bash
#SBATCH --job-name=instrain
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=08:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=4G

module load bio-apps/v202603
module load py-instrain/1.6.3

inStrain profile aligned.sorted.bam genomes.fasta -o instrain_out -p $SLURM_CPUS_PER_TASK

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

More information