modules/canu

Accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads.

Assemblypacbiohifinanopore

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

Description

Accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads.

Input

name:type

description

pattern

`meta:map`

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

`reads:file`

fasta/fastq file

*.{fasta,fastq}

`mode:string`

Canu mode depending on the input data (source and error rate)

-pacbio|-nanopore|-pacbio-hifi

`genomesize:string`

An estimate of the size of the genome. Common suffices are allowed, for example, 3.7m or 2.8g

<number>[g|m|k]

Output

name:type

description

pattern

`report`

`meta:map`

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

`*.report:file`

Most of the analysis reported during assembly

*.report

`assembly`

`meta:map`

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

`*.contigs.fasta.gz:file`

Everything which could be assembled and is the full assembly, including both unique, repetitive, and bubble elements.

*.contigs.fasta

`contigs`

`meta:map`

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

`*.unassembled.fasta.gz:file`

Reads and low-coverage contigs which could not be incorporated into the primary assembly.

*.unassembled.fasta

`corrected_reads`

`meta:map`

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

`*.correctedReads.fasta.gz:file`

The reads after correction.

*.correctedReads.fasta.gz

`corrected_trimmed_reads`

`meta:map`

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

`*.trimmedReads.fasta.gz:file`

The corrected reads after overlap based trimming

*.trimmedReads.fasta.gz

`metadata`

`meta:map`

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

`*.contigs.layout:file`

(undocumented)

*.contigs.layout

`contig_position`

`meta:map`

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

`*.contigs.layout.readToTig:file`

The position of each read in a contig

*.contigs.layout.readToTig

`contig_info`

`meta:map`

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

`*.contigs.layout.tigInfo:file`

A list of the contigs, lengths, coverage, number of reads and other metadata. Essentially the same information provided in the FASTA header line.

*.contigs.layout.tigInfo

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

canu
GPL v2 and others

Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing.

canu.readthedocs.io/en/latest/index.html# canu.readthedocs.io/en/latest/tutorial https://github.com/marbl/canu 10.1101/gr.215087.116