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

]

reads (file)

List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively in gzipped or uncompressed FASTQ or FASTA format.

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

contigs (file)

Final final contigs result of the assembly in FASTA format.

*.contigs.fa.gz

k_contigs (file)

Contigs assembled from the de Bruijn graph of order-K

k*.contigs.fa.gz

addi_contigs (file)

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

k*.addi.fa.gz

local_contigs (file)

Contigs of the locally assembled contigs for k=K

k*.local.fa.gz

kfinal_contigs (file)

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

k*.final.contigs.fa.gz
maintainer
Github user jfy133
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

megahit
GPL v3

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

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