BWA-SW algorithm for single-end reads

Description

Aligns single end reads to selected reference genome using the BWA_SW algorithm. The reads have to be supplied in fastq format.

Parameters

Details

This tool uses BWA short read aligner to align a set of FASTQ formatted sequences against a reference genome. Aligning is performed with Burrows-Wheeler Transform based BWA-SW algorithm that allows gaps in the alignments. This algorithm is designed for longer reads (>200 bp) than the BWA aln algorithm. It performs heuristic Smith-Waterman-like alignment to find high-scoring local hits.

Note that this aligner is more accurate but significantly slower than Bowtie

Output

As a result the tool returns a sorted and indexed BAM-formatted alignment, which is ready for viewing in the Chipster genome browser.