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
versions.yml: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
