bowtie2Build: Creates index on reference genome using bowtie2-build

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

Description

Creates index on reference genome using bowtie2-build.

Usage

## Default S3 method:
bowtie2Build(pathnameFAs, bowtieRefIndexPrefix, optionsVec=NULL, ...,
  command="bowtie2-build", verbose=FALSE)

Arguments

pathnameFAs	A character vector of FASTA reference files.
bowtieRefIndexPrefix	A character string specifying the bowtie2 reference index to be built (partial pathname, minus the .*.bt2 suffix).
optionsVec	(optional) A named character vector.
...	...
command	The name of the external executable.
verbose	See Verbose.

Support for compressed input files

If gzipped FASTA files are used, this function will temporarily decompress before passing them to the bowtie2-build external software (which only support non-compressed FASTA files).

Known issues

The FASTA pathnames must not contain commas. If detected, this method generates an informative error.

Author(s)

Henrik Bengtsson, Taku Tokuyasu

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