doBWA: Read alignment using the Burrows-Wheeler Transform aligner...

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

Description

Read alignment using the Burrows-Wheeler Transform aligner (BWA) based on [1].

Usage

  doBWA(...)
  ## S3 method for class 'AromaSeqDataFileSet'
doBWA(dataSet, reference, ..., verbose=FALSE)

Arguments

dataSet, df	A FastqDataSet or a BamDataSet.
reference	A FastaReferenceFile or a BwaIndexSet specifying the genome reference to align the FASTQ reads to.
...	Additional arguments passed to BwaAlignment.
verbose	See Verbose.

Value

Returns a BamDataSet.

Author(s)

Henrik Bengtsson

References

[1] Li H. and Durbin R., Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 2009.
[2] Li H. and Durbin R., Fast and accurate long-read alignment with Burrows-Wheeler Transform. Bioinformatics, 2010.

See Also

For more details, see BwaAlignment.

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