A comparison of alignment throughput of BWA and BarraCUDA in align real-life sequencing reads to the human genome. Two whole-genome shotgun libraries from the 1000 Genomes Project were used to compare the paired-end alignment throughput between BWA and BarraCUDA. A. 11.3 million pairs of 37 bp reads (ENA accession: ERR003014) were aligned to the human genome (NCBI 36.54) using BWA v0.5.8 with a server class Intel Xeon 5670 (utilising 1 or 6 threads) and BarraCUDA with an NVIDIA Tesla M2090, both with default options. The figure shows the time taken for 'aln' core (in blue) and 'sampe' core (in red); B. The time taken with gap opening disabled using the option '-o 0'; C. The time taken to align 14.5 million pairs of 76 bp reads (ENA accession: SRR032215) using the same set of hardware; D. The timings with gap opening disabled.