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

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.

Pubmed ID: 19561018 RIS Download

Mesh terms: Algorithms | Chromosome Breakpoints | Computational Biology | DNA Breaks | Genome | INDEL Mutation | Sequence Analysis, DNA | Software

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SAMTOOLS

Software tool for manipulating alignments in SAM format for storing nucleotide sequence alignment, including sorting, merging, indexing and generating alignments in per position format. Parts that are relevant to genetic analysis include SNP and indel callings.

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European Bioinformatics Institute

Non-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL.

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