TreQ: Indel-tolerant read mapping

TreQ is a read mapper for high-throughput DNA sequencing reads, in particular reads from 100 nt to hundreds of nucleotides, and for large edit distance between sequencing read and match in the reference genome. In contrast to existing read mappers, TreQ can cope particularly well with indels, either one long indel; see the figure giving the percentage of accurate matches as a function of indel length for 200 nt reads. TreQ performs best at a time comparable to BWA at large edit distance settings, SSAHA2 is the second best but is five times slower than tree. This makes TreQ an excellent choice for analyzing genetic variants in low-coverage situations and without the need for paired-end sequencing. TreQ will be released under the GPL upon publication.

For further information see the main website at or contact Md P. Mahmud ( This software is a result of or used in the following projects: HTSMethods, TreqCG, AlgoEngineering.


Members: Md P. Mahmud, Alexander Schliep, Md P. Mahmud, John Wiedenhoeft.


Mahmud. Reduced representations for efficient analysis of genomic data; from microarray to high throughput sequencing. Ph.D. Thesis, Oct 2014.