megahit¶
Purpose¶
This components assembles metagenomic paired-end FastQ files using the megahit assembler.
Note
Software page: https://github.com/voutcn/megahit
Input/Output type¶
- Input type:
FastQ
- Output type:
Fasta
Note
The default input parameter for FastQ data is --fastq
. You can change
the --fastq
parameter default pattern (fastq/*_{1,2}.*
) according
to input file names (e.g.: --fastq "path/to/fastq/*R{1,2}.*"
).
Parameters¶
megahitKmers
: If ‘auto’ the megahit k-mer lengths will be determined from the maximum read length of each assembly. If ‘default’, megahit will use the default k-mer lengths.fastg
: When true, it converts megahit intermediate contigs into fastg. Default: False
Published results¶
results/assembly/megahit
: Stores the fasta assemblies for each sample.
Published reports¶
None.
Default directives¶
cpus
: 4memory
: 5GB (dynamically increased on retry)container
: cimendes/megahitversion
: v1.1.3-0.1scratch
: true