bwaAln: BWA-backtrack alignment via 'bwa aln'

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

Description

BWA-backtrack alignment via 'bwa aln'.

Usage

## Default S3 method:
bwaAln(pathnameFQ, indexPrefix, pathnameD, ..., verbose=FALSE)

Arguments

pathnameFQ	The FASTQ file to be aligned.
indexPrefix	The pathname prefix to the BWA index files.
...	Additional arguments specifying BWA 'aln' switches passed to systemBWA().
pathnameD	The destination pathname.
verbose	See Verbose.

Author(s)

Henrik Bengtsson

Examples

## Not run: 
  pathnameFA <- "annotationData/organisms/Lambda_phage/lambda_virus.fa"
  bwaIndex(pathnameFA)
  indexPrefix <- bwaIndexPrefix(pathnameFA)
  bwaAln("fastqData/LambdaVirusExample/Lambda_phage/reads_1.fq",
         indexPrefix=indexPrefix,
         pathnameD="fastqData/LambdaVirusExample/Lambda_phage/reads_1.sai")

## End(Not run)

HenrikBengtsson/aroma.seq documentation built on Feb. 15, 2021, 2:21 a.m.