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. 2013 Aug 15;29(16):2041-3.
doi: 10.1093/bioinformatics/btt314. Epub 2013 Jun 4.

Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms

Come Raczy  1 , Roman Petrovski, Christopher T Saunders, Ilya Chorny, Semyon Kruglyak, Elliott H Margulies, Han-Yu Chuang, Morten Källberg, Swathi A Kumar, Arnold Liao, Kristina M Little, Michael P Strömberg, Stephen W Tanner
Affiliations

Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms

Come Raczy et al. Bioinformatics. .

Abstract

Summary: An ultrafast DNA sequence aligner (Isaac Genome Alignment Software) that takes advantage of high-memory hardware (>48 GB) and variant caller (Isaac Variant Caller) have been developed. We demonstrate that our combined pipeline (Isaac) is four to five times faster than BWA + GATK on equivalent hardware, with comparable accuracy as measured by trio conflict rates and sensitivity. We further show that Isaac is effective in the detection of disease-causing variants and can easily/economically be run on commodity hardware.

Availability: Isaac has an open source license and can be obtained at https://github.com/sequencing.

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Comment in

  • Reference bias in the Illumina Isaac aligner.
    Cornish AJ, Chubb D, Frangou A, Hoang PH, Kaiser M, Wedge DC, Houlston RS. Cornish AJ, et al. Bioinformatics. 2020 Nov 1;36(17):4671-4672. doi: 10.1093/bioinformatics/btaa514. Bioinformatics. 2020. PMID: 32437525 Free PMC article. No abstract available.