bwa: Wrapper for BWA sequence alignment tool

In flow-r/ngsflows: Robust Pipelines for Next-Generation Sequencing Analysis; A Companion Package for flowr

Description

Quoting from BWA's website:

BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads. For all the algorithms, BWA first needs to construct the FM-index for the reference genome (the index command). Alignment algorithms are invoked with different sub-commands: aln/samse/sampe for BWA-backtrack, bwasw for BWA-SW and mem for the BWA-MEM algorithm.

Usage

bwa(method = c("backtrack", "mem", "aln_sam"), ...)

bwa.backtrack(fqs1, fqs2, paired_end,
  samplename = opts_flow$get("samplename"),
  bwa_exe = opts_flow$get("bwa_exe"), ref_bwa = opts_flow$get("ref_bwa"),
  bwa_aln_opts = opts_flow$get("bwa_aln_opts"),
  cpu_bwa_aln = opts_flow$get("cpu_bwa_aln"),
  bwa_sampe_opts = opts_flow$get("bwa_sampe_opts"),
  bwa_samse_opts = opts_flow$get("bwa_samse_opts"),
  samtools_exe = opts_flow$get("samtools_exe"))

bwa.mem(fqs1, fqs2, paired_end = opts_flow$get("paired_end"),
  samplename = opts_flow$get("samplename"),
  bwa_exe = opts_flow$get("bwa_exe"), ref_bwa = opts_flow$get("ref_bwa"),
  bwa_mem_opts = opts_flow$get("bwa_mem_opts"),
  cpu_bwa_mem = opts_flow$get("cpu_bwa_mem"),
  samtools_exe = opts_flow$get("samtools_exe"), execute = FALSE)

Arguments

bwa_mem_opts
fastq1	character vector with full paths to fastq files for mate 1.
fastq2	character vector

Value

A list, with cmds as one of the variables which contains system commands to be run.

Source

http://bio-bwa.sourceforge.net/bwa.shtml

flow-r/ngsflows documentation built on May 16, 2019, 1:25 p.m.