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

By C. Raczy, Roman Petrovski, Christopher T. Saunders, I. Chorny, S. Kruglyak, Elliott H. Margulies, Han-Yu Chuang, Morten Källberg, Swathi A. Kumar, A. Liao and 3 more. Bioinform., 2013

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Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications (2014, background): “The most common approach is to map reads to a reference genome 6,10–13 and either scan for systematic differences with the reference or identify haplotypes that are well supported by the data 14 .”
Detection of long repeat expansions from PCR-free whole-genome sequence data (2016, background): “Variant callers for small variants such as single nucleotide polymorphisms and small insertions or deletions typically require multiple reads to completely span the full length of the non-reference allele (Raczy et al. 2013; DePristo et al. 2011).”
A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree (2016, neutral): “We included variant calls from six different informatics pipelines (Conrad et al. 2011; Garrison and Marth 2012; Iqbal et al. 2012; Saunders et al. 2012; Raczy et al. 2013; Rimmer et al. 2014) and two different sequencing technologies (Bentley et al.”
Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer. (2018, positive): “Reads were aligned against hg38-decoy using the Isaac aligner version 04.17.06.15 (Raczy et al., 2013).”