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

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


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

MeSH terms

  • Genetic Variation
  • Genome, Human
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / methods*
  • Software*