Description

inStrain is python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information e.g. [ id:‘test’]

bam (path)

Path to .bam file to be profiled

*.{bam,sam}

genome_fasta (path)

Path to .fasta file to be profiled; MUST be the .fasta file that was mapped to to create the .bam file

*.{fasta,fna,fa}

genes_fasta (path)

Path to .fna file of genes to be profiled (OPTIONAL)

*.{fasta,fna,fa}

stb_file (path)

Path to .stb (scaffold to bin) file to be profiled (OPTIONAL)

*.stb

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

profile (path)

InStrain profile folder

*.IS/
author
Github user mrolm
get in touch
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Tools

instrain
MIT

Calculation of strain-level metrics

github.com/MrOlm/instrain instrain.readthedocs.io/en/latest https://github.com/MrOlm/instrain 10.1038/s41587-020-00797-0