BWA for single end reads and own genome


Aligns single 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 FASTQ format.



This tool uses BWA short read aligner to align a set of FASTQ formatted sequences against a FASTA formatted reference sequence. Aligning is performed with Burrows-Wheeler Transform based BWA aln algoritm that allows gaps in the alignments. This algorithm is designed for short queries up to ~200bp with low error rate (<3%).

It is possible to give the tool more than one FASTQ file. The tool will run the alignment for each file separately, and finally merge the resulting BAM files.

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


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