simMC (≥ 10 reads): semi-supervised setting. OFDEG+GC and tetranucleotide frequency (TF) comparison using semi-supervised methods, for the Phrap (A) and Arachne (B) assemblers. We observe these results to be of a similar trend to the 8 kbp tests, yet we experience a much more profound reduction in specificity on the Phrap data set. We attribute this to the shorter fragments contained in the Phrap data set, which further contributes to the amibiguity in association between genomic fragment and parent organism.
Saeed and Halgamuge BMC Genomics 2009 10(Suppl 3):S10 doi:10.1186/1471-2164-10-S3-S10