Description

An ultra-fast metagenomic assembler for large and complex metagenomics

Input

name:type
description
pattern

meta{:bash}

: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{:bash}

: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{:bash}

: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{:bash}

meta{:bash}

:map

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

*.contigs.fa.gz{:bash}

:file

Final final contigs result of the assembly in FASTA format.

*.contigs.fa.gz

k_contigs{:bash}

meta{:bash}

:map

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

intermediate_contigs/k*.contigs.fa.gz{:bash}

:file

Contigs assembled from the de Bruijn graph of order-K

k*.contigs.fa.gz

addi_contigs{:bash}

meta{:bash}

:map

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

intermediate_contigs/k*.addi.fa.gz{:bash}

:file

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

k*.addi.fa.gz

local_contigs{:bash}

meta{:bash}

:map

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

intermediate_contigs/k*.local.fa.gz{:bash}

:file

Contigs of the locally assembled contigs for k=K

k*.local.fa.gz

kfinal_contigs{:bash}

meta{:bash}

:map

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

intermediate_contigs/k*.final.contigs.fa.gz{:bash}

:file

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

k*.final.contigs.fa.gz

log{:bash}

meta{:bash}

:map

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

*.log{:bash}

:file

Log file containing statistics of the assembly output

*.log

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

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
included in
magviralmetagenome
maintainer
Github user jfy133
get in touch
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