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:file

Path to .bam file to be profiled

*.{bam,sam}

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:type
description
pattern

profile

meta:map

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

]

*.IS:directory

InStrain profile folder

*.IS/

snvs

meta:map

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

]

*.IS/output/*.IS_SNVs.tsv:file

SNVs

*.tsv

gene_info

meta:map

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

]

*.IS/output/*.IS_gene_info.tsv:file

Gene information

*.tsv

genome_info

meta:map

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

]

*.IS/output/*.IS_genome_info.tsv:file

Genome information

*.tsv

linkage

meta:map

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

]

*.IS/output/*.IS_linkage.tsv:file

Linkage information

*.tsv

mapping_info

meta:map

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

]

*.IS/output/*.IS_mapping_info.tsv:file

Mapping information

*.tsv

scaffold_info

meta:map

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

]

*.IS/output/*.IS_scaffold_info.tsv:file

Scaffold information

*.tsv

versions

versions.yml:file

File containing software versions

versions.yml

Tools

included in
phageannotator
maintainer
Github user mrolm
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