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
: 1memory
: 5GB (dynamically increased on retry)container
: flowcraft/bowtie2_samtoolsversion
: 1.0.0-1
bowtie
:cpus
: 4memory
: 5GB (dynamically increased on retry)container
:flowcraft/bowtie2_samtoolsversion
: 1.0.0-1