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

Bioinformatics. 2009 Nov 1;25(21):2865-71. doi: 10.1093/bioinformatics/btp394. Epub 2009 Jun 26.


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 approximately kye/pindel/.


Ye K, Schulz MH, Long Q, Apweiler R, Ning Z.

Institute Authors