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
Description
Pattern

0 ()

1 ()

genome_fasta (file)

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 (file)

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

*.{fasta,fna,fa}

stb_file (file)

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

*.stb

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

Tools

instrain Documentation

Calculation of strain-level metrics

https://github.com/MrOlm/instraindoi: 10.1038/s41587-020-00797-0License: MIT
Authors