BWA for paired-end reads and own genome

Description

Aligns paired-end reads to the reference genome sequence given by the user. The alignment is constructed using the BWA aln algorithm. The genome needs to be supplied in fasta format and the reads in two fastq files.

Parameters

Details

This tool uses BWA short read aligner to align two sets of FASTQ formatted sequences against a fasta-formatted reference sequence. The first read file should contain all the first reads of the read pairs and the second read file all the pairs for the first reads in the same order as in the first read file.

A BWA index is automatically calculated for the given reference genome or sequence set. Aligning is performed with the Burrows-Wheeler Transform based aln algorithm that allows gaps in the alignments.

Output

As a result the tool returns a sorted and indexed BAM-formatted alignment.