Software accompaniment to
Bresler, M., Sheehan, S., Chan, A.H., and Song, Y.S. Telescoper: De novo Assembly of Highly Repetitive Regions. ECCB'12 Special Issue, Bioinformatics, 28 (2012) i311-i317.
Telescoper is a local assembly algorithm designed for short-reads from NGS platforms such as Illumina. The reads must come from two libraries: one short insert, and one long insert. The algorithm begins with a user-given seed string, and assembles a graph of possible extensions, and prints one path of extensions, as a fasta file.
The software is still a beta version. We have not yet tested it extensively, and envision many improvements down the line.
This software is available under the Berkeley Software Distribution License. Please see the "BSD License" file included for further details.
Source code (version 0.2) (November, 2012)
Example (TelescoperSrcWithExample.tar.gz) contains the source code as well. For those who downloaded Rel_1, that was the same as the present file, just with a less informative name. The older version 0.1 had an error in the read preproccessing file, introduced in the course of clarifying the code, for which I'm very sorry.
If you have any questions about the Telescoper software, please contact Ma'ayan Bresler (email@example.com). The corresponding author for the paper is Yun S. Song (firstname.lastname@example.org).