Statistics of alignment with three different sequence alignment tools.

Illumina® MiSeq reads were aligned with three different statistical alignment methods to compare ease of use and computational time. Reads for a variant library 65 bp in length with 50,625 members were processed using the graphaligner, Smith-Waterman alignment, and Bowtie 2 (Bt2). The number of references N, mapping rate, map time to process 1 million reads, the percent suboptimal mappings and the relative speed are shown. The build times for the FSM in the graphaligner and the Bowtie 2 FM-index (an index of the full-text substrings from the regular expression representation of the library, which is compressed and allows for fast substring queries) [23] are included in the read rates and are negligible. We have estimated the metrics for 50,625 references for Smith-Waterman from a run with 1000 references, due to the large computational time for 50,625 references.