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

By Kai Ye, Marcel H. Schulz, Quan Long, Rolf Apweiler, Zemin Ning. Bioinform., 2009

2,074 citations recorded by the source corpus.

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/∼kye/pindel/. Contact: k.ye@lumc.nl; zn1@sanger.ac.uk

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c9822d68e54990cd24bbfbd981e43ea9898d96ec

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

Citations in the corpus

Best practices for variant calling in clinical sequencing (2020, methodology): “Structural variants DELLY [51], Lumpy [52], Manta [53], Pindel [54], SVMerge [55]”
Dindel: accurate indel calls from short-read data. (2011, methodology): “However, it is possible to detect large deletions through split-read approaches (Ye et al. 2009) or small insertions using paired-end sequencing and mapping.”
The Next-Generation Sequencing Revolution and Its Impact on Genomics (2013, neutral): “…algorithms have been developed for the detection and genotyping of germline SNPs (DePristo et al., 2011; Koboldt et al., 2009; Li et al., 2008; McKenna et al., 2010; Shen et al., 2010) and small indels (Emde et al., 2012; Leone et al., 2013; Ye et al., 2009) in high-throughput sequencing data.”
Pathogenic germline variants in 10,389 adult cancers (2018, methodology): “Michael Seiler, Peter G. Smith, Ping Zhu, Silvia Buonamici, and Lihua Yu are employees of H3 Biomedicine, Inc. Parts of this work are the subject of a patent application: WO2017040526 titled ‘‘Splice variants associated with neomorphic sf3b1 mutants.’’”
Heterogeneity of genomic evolution and mutational profiles in multiple myeloma (2014, positive): “To call insertions and deletions, we used split-read mapping implemented as a modiﬁcation of the Pindel algorithm 56 .”
The Sequence of 1504 Mutants in the Model Rice Variety Kitaake Facilitates Rapid Functional Genomic Studies (2017, background): “Due to the nature of variant calls made by the algorithms (Ye et al., 2009), our results only included tandem duplications but not dispersed duplications.”