BWA is a reference mapper for short read data. It maps short reads to a given reference genomes. BWA contains several algorithms, the implementation in SeqSphere+ uses the bwa-sw algorithm (version 0.6.1/0.6.2 for windows/linux).
The BWA Reference Mapper can be directly accessed using the menu Tools | Short Read Mapper (BWA-SW). The reference mapper reads from FASTQ-files that contain either single or paired reads. The input files can be quality trimmed and downsampled before mapping. The mapped reads and the reference sequence are stored in a BAM-file. Reference mapping will work with most short read data. Compared to de-novo assembling it is fast and needs only a limited amount of memory. However, results depend on the chosen reference sequence. Therefore, reference mapping produces good results for monomorphic organisms (e.g. M. tuberculosis) or for Samples that are closely related to the isolate from which the reference sequence is taken. ContentsQuality TrimmingThe reads can be processed before they are mapped. They can be automatically trimmed based on read quality and downsampled. BWA does its own trimming, so quality trimming is disabled by default. When trimming is enabled, reads are trimmed on both ends until the average base quality is better than the given value in a window of a selected number of bases. DownsamplingTo reduce the size of the output files and the time required for mapping, the input files can be downsampled. Downsampling randomly removes reads so that the given approx. size is obtained. If quality trimming is selected, downsampling is done on the trimmed reads. Standard Settings (in pipeline and manual mode)
Manual Settings (in manual mode only)
PostprocessingBefore a BAM file can be scanned by SeqSphere+, a consensus sequence is automatically calculated by the built in consensus caller. Speed and MemoryReference mapping does not require huge amounts of memory, 4GB is usually sufficient. Depending on genome size, read count, and read lengths reference mapping may take from 10 to 40 minutes or longer on a fast quad-core computer (in 2013).
Open Source noteThe BWA reference mapping function is a wrapper to an external BWA executable. This BWA executable is open source software that is licensed under the GNU General Public License version 3.0 (GPLv3). The program homepage is: http://bio-bwa.sourceforge.net/. The windows version of BWA is from here: http://bow.codeplex.com/. The source code is installed next to the executable. For more information on BWA, see: Li H. and Durbin R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler Transform. Bioinformatics, Epub. [PMID: 20080505] |