Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Ye, K., Schulz, M. H., Long, Q., Apweiler, R., & Ning, Z. Bioinformatics (Oxford, England), 25(21):2865–2871, November, 2009. doi abstract bibtex 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: k.ye@lumc.nl; zn1@sanger.ac.uk.
@article{ye_pindel_2009,
title = {Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads},
volume = {25},
issn = {1367-4811},
shorttitle = {Pindel},
doi = {10.1093/bioinformatics/btp394},
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: k.ye@lumc.nl; zn1@sanger.ac.uk.},
language = {eng},
number = {21},
journal = {Bioinformatics (Oxford, England)},
author = {Ye, Kai and Schulz, Marcel H. and Long, Quan and Apweiler, Rolf and Ning, Zemin},
month = nov,
year = {2009},
pmid = {19561018},
pmcid = {PMC2781750},
keywords = {Algorithms, Chromosome Breakpoints, Computational Biology, DNA Breaks, Genome, INDEL Mutation, Sequence Analysis, DNA, Software},
pages = {2865--2871},
file = {Volltext:/Users/mschulz/Zotero/storage/IZVKUL3B/Ye et al. - 2009 - Pindel a pattern growth approach to detect break .pdf:application/pdf},
}
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