modules/megahit

An ultra-fast metagenomic assembler for large and complex metagenomics

megahitdenovoassemblydebruijnmetagenomics

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

Description

An ultra-fast metagenomic assembler for large and complex metagenomics

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information and input single, or paired-end FASTA/FASTQ files (optionally decompressed) e.g. [ id:‘test’, single_end:false ]

`reads1`
`:file`

A single or list of input FastQ files for single-end or R1 of paired-end library(s), respectively in gzipped or uncompressed FASTQ or FASTA format.

`reads2`
`:file`

A single or list of input FastQ files for R2 of paired-end library(s), respectively in gzipped or uncompressed FASTQ or FASTA format.

Output

name:type

description

pattern

`contigs`

`meta`
`:map`

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

`*.contigs.fa.gz`
`:file`

Final final contigs result of the assembly in FASTA format.

*.contigs.fa.gz

`k_contigs`

`meta`
`:map`

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

`intermediate_contigs/k*.contigs.fa.gz`
`:file`

Contigs assembled from the de Bruijn graph of order-K

k*.contigs.fa.gz

`addi_contigs`

`meta`
`:map`

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

`intermediate_contigs/k*.addi.fa.gz`
`:file`

Contigs assembled after iteratively removing local low coverage unitigs in the de Bruijn graph of order-K

k*.addi.fa.gz

`local_contigs`

`meta`
`:map`

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

`intermediate_contigs/k*.local.fa.gz`
`:file`

Contigs of the locally assembled contigs for k=K

k*.local.fa.gz

`kfinal_contigs`

`meta`
`:map`

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

`intermediate_contigs/k*.final.contigs.fa.gz`
`:file`

Stand-alone contigs for k=K; if local assembly is turned on, the file will be empty

k*.final.contigs.fa.gz

`log`

`meta`
`:map`

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

`*.log`
`:file`

Log file containing statistics of the assembly output

*.log

`versions_megahit`

`${task.process}`
`:string`

The name of the process

`megahit`
`:string`

The name of the tool

`megahit -v | sed 's/MEGAHIT v//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`megahit`
`:string`

The name of the tool

`megahit -v | sed 's/MEGAHIT v//'`
`:eval`

The expression to obtain the version of the tool

Tools

megahit
GPL v3

An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

args_id: $args

github.com/voutcn/megahit 10.1093/bioinformatics/btv033

pigz

Parallel implementation of the gzip algorithm.

args_id: $args2

zlib.net/pigz zlib.net/pigz/pigz.pdf