title: Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  Isaac has an open source license and can be obtained at https://github.com/sequencing.
authors.affiliation: Illumina United Kingdom, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex, UK. craczy@illumina.com
authors.forename: Come
authors.initials: C
authors.lastname: Raczy
authors.forename: Roman
authors.initials: R
authors.lastname: Petrovski
authors.forename: Christopher T
authors.initials: CT
authors.lastname: Saunders
authors.forename: Ilya
authors.initials: I
authors.lastname: Chorny
authors.forename: Semyon
authors.initials: S
authors.lastname: Kruglyak
authors.forename: Elliott H
authors.initials: EH
authors.lastname: Margulies
authors.forename: Han-Yu
authors.initials: HY
authors.lastname: Chuang
authors.forename: Morten
authors.initials: M
authors.lastname: Källberg
authors.forename: Swathi A
authors.initials: SA
authors.lastname: Kumar
authors.forename: Arnold
authors.initials: A
authors.lastname: Liao
authors.forename: Kristina M
authors.initials: KM
authors.lastname: Little
authors.forename: Michael P
authors.initials: MP
authors.lastname: Strömberg
authors.forename: Stephen W
authors.initials: SW
authors.lastname: Tanner
mesh_terms: D014644:Genetic Variation; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software