bowtie2: bowtie2

In omicsCore/SEQprocess: SEQprocess : a modularized and customizable pipeline framework for NGS processing in R package.

Description

A wrapper function to run bowtie2.

Usage

bowtie2(fq1, output.dir, sample.name, bowtie.idx, mc.cores=1, run.cmd=TRUE)

Arguments

fq1	Path to read1 fastq files
output.dir	Output directory
sample.name	A character vector for the sample names
bowtie.idx	Path to bowtie index files
mc.cores	The number of cores to use. Must be at least one(default=1), and parallelization requires at least two cores.
run.cmd	Whether to execute the command line (default=TRUE)

Details

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. Bowtie2 is used only for single-end sequencing data.

Value

Aligned SAM files

References

Fast gapped-read alignment with Bowtie 2

See Also

http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

omicsCore/SEQprocess documentation built on May 7, 2020, 4:18 a.m.