Alignment comparison using HiSeq 2000, 454 and Ion Torrent reads. (a–d) Bowtie 2, BWA, SOAP2 and Bowtie were used to align two million 100 nt × 100 nt paired-end HiSeq 2000 reads from a resequencing study. Shown are results for unpaired alignment of end 1 (a), paired-end alignment (b), Bowtie 2 and BWA-SW alignment of 1 million 454 reads from the 1000 Genomes Project Pilot (c), and Bowtie 2 and BWA-SW to align one million Ion Torrent reads from the G. Moore resequencing project (d). Plotted is the percentage of reads for which at least one alignment was found. Each numbered point is data obtained using command-line parameters shown in .