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remove_host.rst

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remove_host

Purpose

This component performs a mapping procedure of FastQ files using a host genome as referece (default: hg19). The procedure is carried out with bowtie2 and samtools and aims to filter the reads that map to host genome.

Note

- bowtie2 documentation can be found here. - samtools documentation can be found here.

Input/Output type

  • Input type: FastQ
  • Output type: FastQ

Note

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

Parameters

- refIndex: Specifies the reference indexes to be provided to bowtie2. Default: '/index_hg19/hg19' (from docker image).

Published results

  • results/mapping/: A txt file from bowtie2 with the mapping statistics.

Published reports

None.

Default directives

  • remove_host:
    • cpus: 3
    • memory: 5GB (dynamically increased on retry)
    • container: flowcraft/remove_host
    • version: 2-0.1

Advanced

Template

assemblerflow.templates.remove_host