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: 4
  • memory: 5GB (dynamically increased on retry)
  • container: cimendes/megahit
  • version: v1.1.3-0.1
  • scratch: true

Advanced

Template

assemblerflow.templates.megahit