Burrow-Wheeler Aligner (BWA)

Burrow-Wheeler Aligner (BWA) | findAIList | Find AI List

Overview

BWA (Burrow-Wheeler Aligner) is a software suite designed for mapping DNA sequences to a large reference genome. It includes three primary algorithms: BWA-backtrack (for Illumina reads up to 100bp), BWA-SW (for longer sequences from 70bp to a few megabases), and BWA-MEM (the latest and generally recommended algorithm, faster and more accurate than the others). BWA first constructs an FM-index for the reference genome. Alignment algorithms are invoked via sub-commands: aln/samse/sampe (BWA-backtrack), bwasw (BWA-SW), and mem (BWA-MEM). BWA-MEM has been largely replaced by minimap2 for long-read alignment (PacBio and Nanopore), however BWA-MEM2 offers significant speed improvements over BWA-MEM. The tool is available under the GPLv3 license.

Common tasks

DNA Sequence Alignment Reference Genome Mapping Short-Read Alignment Long-Read Alignment

FAQ

View all

What types of data does BWA work with?

BWA works with various types of DNA sequence data, including Illumina, 454, IonTorrent, PacBio, and Oxford Nanopore reads. The optimal algorithm and settings may vary depending on the data type and read length.

Why does a read appear multiple times in the output SAM?

BWA-SW and BWA-MEM perform local alignments. If there is a translocation, a gene fusion, or a long deletion, a read bridging the breakpoint may have two hits, occupying two lines in the SAM output.

Does BWA work on reference sequences longer than 4GB in total?

Yes, BWA can handle reference sequences longer than 4GB.

Why can one read in a pair have high mapping quality but the other has zero?

This can occur due to various reasons, such as adapter contamination, poor quality in one of the reads, or structural variations.

FAQ+