Bowtie and UGENE Genome Aligner

UGENE contains plugin UGENE genome aligner and graphical port of short read aligner Bowtie.

UGENE genome aligner is fast short read aligner. It aligns DNA sequences of various length to the reference genome with configurable mismatch rate.

Bowtie packages are integrated completely, so there is no need in extra files for using these tools.

Bowtie is not configurable yet and uses only default settings (-n 2 -l 28 -e 70). About bowtie configuration can be read on bowtie manual page.

To run Bowtie or UGENE genome aligner use the "Tools->DNA Assembly" menu, select assembly method "Bowtie".

The dialog contains list of available dna assembly algorithms "Bowtie", "UGENE genome aligner", fields for reference sequence file, result alignment file, number of allowed mismatches (only for UGENE genome aligner) and short reads files.

To start assembly select files with reference sequence and short reads, then press button "Start Assembly".

For short reads can be selected multiple number of files that contains DNA sequences.

Note, that for Bowtie reads lenght can't be more than 1024. UGENE genome aligner has no limitation for reads length.

Bowtie plugin can use prebuilt index file, to use prebuild index select file with .ebwt extension.

If selected sequence file, Bowtie will built index and output a set of 6 files with suffixes .1.ebwt, .2.ebwt, .3.ebwt, .4.ebwt, .rev.1.ebwt, and .rev.2.ebwt  in result file path. This files can be later selected as prebuilt index.