modules/cobrameta

A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.

cobracontigscaffoldassemblyextensionvirusphage

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

Description

A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.

Input

name:type

description

pattern

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`fasta:file`

Assembly file (contigs/scaffolds) in FASTA format

*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz}

`meta2:map`

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

]

`coverage:file`

TSV file with 2 columns containing 1) the contig/scaffold id and 2) the coverage depth of the sequence specified in column 1

*.{tsv,txt}

`meta3:map`

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

]

`query:file`

File containing the query contigs that the user wants COBRA to extend. This can be provided in one-column TXT or FASTA format. (The IDs must match the IDs in the --fasta file exactly)

*.{txt,fasta}

`meta4:map`

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

]

`bam:file`

Sorted BAM/CRAM/SAM file resulting from mapping reads used in assembly to the resulting assembly FASTA

*.{bam,cram,sam}

`assembler:string`

The name of the tool used to assemble contigs

{metaspades,megahit,idba}

`mink:integer`

The minimum kmer size used to assemble contigs

[0-9]+

`maxk:integer`

The maximum kmer size used to assemble contigs

[0-9]+

Output

name:type

description

pattern

`self_circular`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`${prefix}/COBRA_category_i_self_circular.fasta.gz:file`

fasta file

*/COBRA_category_i_self_circular.fasta.gz

`extended_circular`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`${prefix}/COBRA_category_ii-a_extended_circular_unique.fasta.gz:file`

Gzipped FASTA file containing query contigs that were joined and extended into a circular genome

${prefix}/COBRA_category_ii-a_extended_circular_unique.fasta.gz

`extended_partial`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`${prefix}/COBRA_category_ii-b_extended_partial_unique.fasta.gz:file`

Gzipped FASTA file containing query contigs were joined and extended, but not into circular sequences

${prefix}/COBRA_category_ii-b_extended_partial_unique.fasta.gz

`extended_failed`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`${prefix}/COBRA_category_ii-c_extended_failed.fasta.gz:file`

Gzipped FASTA file containing query contigs that could not be extended due to COBRA rules

${prefix}/COBRA_category_ii-c_extended_failed.fasta.gz

`orphan_end`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`${prefix}/COBRA_category_iii_orphan_end.fasta.gz:file`

Gzipped FASTA file containing query contigs that do not shared the “expected overlap length” with other contigs

${prefix}/COBRA_category_iii_orphan_end.fasta.gz

`all_cobra_assemblies`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`${prefix}/COBRA_all_assemblies.fasta.gz:file`

Gzipped FASTA file containing all the assemblies generated by COBRA

*/COBRA_all_assemblies.fasta.gz

`joining_summary`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`${prefix}/COBRA_joining_summary.txt:file`

TSV file containing information regarding COBRA’s extension results

${prefix}/COBRA_joining_summary.txt

`log`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`${prefix}/log:file`

Log file containing the contents of each processing

${prefix}/log

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

cobra-meta
MIT

COBRA is a tool to get higher quality viral genomes assembled from metagenomes.

github.com/linxingchen/cobra 10.1038/s41564-023-01598-2