bowtie

Purpose

This component performs a mapping procedure of FastQ files with a given reference. The procedure is carried out with Bowtie2. The reference can a set of Bowtie2 index files or a Fasta file. In the latter, the necessary index will be created with Bowtie2-build and passed through to Bowtie2.

Note

• Bowtie2 documentation can be found here.
• Software page: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

Input/Output type

• Input type: FastQ
• Output type: Bam

Note

The default input parameter for Fastq data is --fastq.

Parameters

• reference: Specifies the reference genome to be provided to to bowtie2-build.
• index: Specifies the reference indexes to be provided to bowtie2.

Note

An index OR a reference fasta file must be provided

Published results

• results/mapping/bowtie: Stores the results of the mapping for each sample.

Published reports

None.

Default directives

• bowtie_build:

  • cpus: 1
  • memory: 5GB (dynamically increased on retry)
  • container: flowcraft/bowtie2_samtools
  • version: 1.0.0-1

• bowtie:

  • cpus: 4
  • memory: 5GB (dynamically increased on retry)
  • container:flowcraft/bowtie2_samtools
  • version: 1.0.0-1