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.

inStrain

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