buildBwaIndexSet.FastaReferenceFile: Builds a BWA index files set

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

Description

Builds a BWA index files set.

Usage

## S3 method for class 'FastaReferenceFile'
buildBwaIndexSet(this, method=c("bwtsw", "is"), ..., skip=TRUE, verbose=FALSE)

Arguments

method	A character string specifying the algorithm to use for building the index set. All methods gives identical results [1]. The default is such that it can handle also large genomes, including the human genome.
...	Additional arguments passed to bwaIndex().
skip	If TRUE, the index files are not rebuilt if already available.
verbose	See Verbose.

Value

Returns a GenericDataFileSet consisting of the BWA index files.

Author(s)

Henrik Bengtsson

References

[1] Thread bwa index option bwtsw, SEQanswers, 2010-07-13. http://seqanswers.com/forums/showthread.php?t=5921
[2] Edwards Bioinformatics Lab, How to create a database for BWA and BWA-SW, 2013. https://edwards.sdsu.edu/research/how-to-create-a-database-for-bwa-and-bwa-sw/
[3] Henrik Bengtsson, bwa index -a is: Details on database 2GB limit?, bwa-help thread on 2013-11-18. https://sourceforge.net/mailarchive/message.php?msg_id=31649355

See Also

Internally, bwaIndex() is used.

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