Up: Component summary Component

Align

This component aligns sequencing reads to the reference genome using the Borrows-Wheeler aligner with the mem algorithm.

Complete documentation:

Version 1.0
Bundle sequencing
Categories Alignment
Authors Amjad Alkodsi (amjad.alkodsi@helsinki.fi)
Issue tracker View/Report issues
Source files component.xml Align.sh
Usage Example with default values

Inputs

Name Type Mandatory Description
reads FASTQ Mandatory Input fastq file for the reads, and can be gzipped
mates FASTQ Mandatory Input fastq file for the mates, and can be gzipped.
reference FASTA Mandatory Reference genome in fasta format. It must be indexed with bwa index

Outputs

Name Type Description
out BAM Output (unsorted) alignment in bam format.

Parameters

Name Type Default Description
ID string (no default) ID of the sequencing run to be written in the bam header in the ID tag. There is no default because it is crucial that you set this correctly and uniquely for each run of your sequencing (one sample can have multiple runs, and each should have a unique ID).
library string "library1" ID of the sequencing run. There is no default because it is crucial that you set this correctly and uniquely for each run of your sequencing (one sample can have multiple runs, and each should have a unique ID).
options string "" Extra options to be passed to the bwa mem command line.
path string "" Path to bwa executable. If empty (default), the executable in your PATH will be used.
platform string "ILLUMINA" Platform name. to be written in the bam header.
sample string (no default) Sample ID to be written in the bam header in the SM tag. There is no default because it is crucial that you set this correctly and uniquely for each of your samples
threads int 1 The number of cpus to be used

Test cases

Test case Parameters IN
reads
IN
mates
IN
reference
OUT
out
case1 properties reads mates reference (missing)

sample=mysample,
ID=myID,
options=-O 7 -E 2 -k 20


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