## 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

- What pre-indexed genome is used as the reference. (Human genome (hg19), Mouse genome (mm9), Rat genome (rn4), Mouse miRBase17.) [Mouse genome]
- Score of a match. Corresponds to the command line parameter -a. [1].
- Gap opening penalty. Corresponds to the command line parameter -q. [11].
- Gap extension penalty. Corresponds to the command line parameter -r. [4].
- Mismatch penalty. Corresponds to the command line parameter -b. [3].
- Band width in the banded alignment. Band width in the banded alignment. Corresponds to the command line parameter -w. [33].
- Minimum score threshold divided by the given value- Corresponds to the command line parameter -T. [37].
- Coefficient for threshold adjustment to query length. Given an l-long query, the threshold for a hit to be retained is a*max{T,c*log(l)}. Corresponds to the command line parameter -c. [5.5].
- Z-best heuristics. Higher -z increases accuracy at the cost of speed. Corresponds to the command line parameter -z. [1].
- Maximum SA interval size for initiating a seed. Higher value increases accuracy at the cost of speed. Corresponds to the command line parameter -s. [3].
- Reverse alignment limit. Minimum number of seeds supporting the resultant alignment to skip reverse alignment. Corresponds to the command line parameter -N. [5].
- How many valid alignments are reported per read. Maximum number of alignments to report. Corresponds to the command line parameter bwa samse -n. [3].

### 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.