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Iterative low-memory k-mer trimming.

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posted on 2014-07-25, 03:13 authored by Qingpeng Zhang, Jason PellJason Pell, Rosangela Canino-Koning, Adina Chuang Howe, C. Titus BrownC. Titus Brown

The results of trimming reads at unique (erroneous) k-mers from a 5 m read E. coli data set (1.4 GB) in under 30 MB of RAM. After each iteration, we measured the total number of distinct k-mers in the data set, the total number of unique (and likely erroneous) k-mers remaining, and the number of unique k-mers present at the 3' end of reads.

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