Bioinformatics · 2013 · 370 citations · 11 references
Life SciencesBioinformaticsGeneticsGenomic Data AnalysisGenomicsSequence AnalysisDna SequencingGenome AlignmentNext-generation SequencingSequence AlignmentVariant AnalysisVariant DetectionAccuracyComputational Efficiency In AlignmentDisease-causing VariantsNext-generation Sequencing AssaysVariant Calling From AlignmentsWhole-genome AlignmentWhole-genome Sequence AnalysisWhole-genome Sequencing Analysis
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. Contact: craczy@illumina.com Supplementary information: Supplementary data are available at Bioinformatics online.
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Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li, Richard Durbin · Bioinformatics · 2009 · 62.8K citations · Full text
Fast and accurate long-read alignment with Burrows–Wheeler transform
Heng Li, Richard Durbin · Bioinformatics · 2010 · 12.9K citations · Full text
A framework for variation discovery and genotyping using next-generation DNA sequencing data
Mark A. DePristo, Eric Banks, Ryan Poplin et al. · Nature Genetics · 2011 · 12.4K citations · Full text
A map of human genome variation from population-scale sequencing