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In a new white paper on our read mapper, we have benchmarked our new read mapping algorithm against our own previous read mapper, and against some of the most popular open source read mappers – BWA, Bowtie2 and SMALT.

Benchmarking has been performed on four human data sets from different sequencing platforms and we can conclude that our read mapper consistently outperforms the market in major disciplines as performance and accuracy.

Highlights from the white paper include mapping of almost 99% of 1.34 billion paired-end Illumina reads in 5 hours, compared to 28 hours for Bowtie2 mapping 99%, 41 hours for SMALT mapping 96%, and 60 hours for BWA mapping 95%.
Our new read mapper scales extremely well with multi-processor machines, enabling up to 35-fold decrease in time to finish a read mapping, and delivers the highest accuracy in almost all the benchmarks discussed in the white paper.

The read mapping algorithm is included in CLC Genomics Workbench, CLC Genomics Server and CLC Assembly Cell.

Download the white paper (PDF)