Phrap UMD consists of the UMD Trimmer, UMD Overlapper and a modified version of Phrap.It is capable of assembling data downloaded directly from the NCBI Trace Archive. The pipeline runs in 3 stages: first the vector ends of the reads are examined and the vector is found. Then the reads are trimmed for vector and quality. After that the trimmed reads afe fed into the 5-pass UMD Overlapper that finds the overlaps, corrects the base caller errors and performs additional trimming if necessary. After the overlaps are produced, the trimmed and error-corrected reads and overlaps are input into the modified version of Phrap, whichonly puts the reads together if they overlap according to the list of overlaps produced by the UMD Overlapper.
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PLoS One. 2008 Mar 19;3(3):e1836.
Improving Phrap-based assembly of the rat using “reliable” overlaps.
Roberts M, Zimin AV, Hayes W, Hunt BR, Ustun C, White JR, Havlak P, Yorke J.