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gen roug for shortcomings; but also requires to develop different algorithms for each platform due to the differ-TS) tec their fi data generated by the Complete Genomics [12] (CG) platform. This is mainly due to the fact that the Complete Genomics company offers only sequencing service, and provides its own analysis results to their customers through the use of proprietary software. The only set of algorithms devised to analyze CG data are described by a group of scientists from the company [13], but the implemen-ds (read se each oth designed sirFAST to efficiently align such reads to the ref assembly, at the presence of the flexible ‘‘expected’ ’ gaps/o within each read. Due to the fact that the Burrows-Wheeler form [15] based methods do not scale well with indels, we imple-mented sirFAST as a hash based seed-and-extend algorithm. Similar to its Illumina and SOLiD based counterparts [16, 17, 18, 19], sirFAST supports both SAM [20] and DIVET [21] file formats. The implementation of sirFAST is publicly available a