modules/instrain_profile

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

instrainmetagenomicspopulation genomicsprofile

https://github.com/nf-core/modules/[...]/modules/nf-core/instrain/profile

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:false ]

`*.IS:directory`

InStrain profile folder

*.IS/

`snvs`

`meta:map`

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

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

SNVs

*.tsv

`gene_info`

`meta:map`

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

`.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:false ]

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

Genome information

*.tsv

`linkage`

`meta:map`

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

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

Linkage information

*.tsv

`mapping_info`

`meta:map`

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

`.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:false ]

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

Scaffold information

*.tsv

`versions`

`versions.yml:file`

File containing software versions

versions.yml

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