Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.

ABSTRACT:

Motivation

There is a strong demand in the genomic community to develop effective algorithms to reliably identify genomic variants. Indel detection using next-gen data is difficult and identification of long structural variations is extremely challenging.

Results

We present Pindel, a pattern growth approach, to detect breakpoints of large deletions and medium-sized insertions from paired-end short reads. We use both simulated reads and real data to demonstrate the efficiency of the computer program and accuracy of the results.

Availability

The binary code and a short user manual can be freely downloaded from http://www.ebi.ac.uk/ approximately kye/pindel/.

Contact

[e-mail]; [e-mail].

SUBMITTER: Ye K 

PROVIDER: S-EPMC2781750 | biostudies-literature | 2009 Nov

REPOSITORIES: biostudies-literature