spades

Purpose

This components assembles paired-end FastQ files using the Spades assembler.

Note

Software page: http://bioinf.spbau.ru/spades

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

  • spadesMinCoverage: The minimum number of reads to consider an edge in the de Bruijn graph during the assembly
  • spadesMinKmerCoverage: Minimum contigs K-mer coverage. After assembly only keep contigs with reported k-mer coverage equal or above this value
  • spadesKmers: If ‘auto’ the SPAdes k-mer lengths will be determined from the maximum read length of each assembly. If ‘default’, SPAdes will use the default k-mer lengths.

Published results

  • results/assembly/spades: Stores the fasta assemblies for each sample.

Published reports

None.

Default directives

  • cpus: 4
  • memory: 5GB (dynamically increased on retry)
  • container: ummidock/spades
  • version: 3.13.0-1
  • scratch: true

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