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Bonnie Hurwitz, Ken Youens-Clark 2016. K-mer-based host screening. protocols.io dx.doi.org/10.17504/protocols.io.ehjbb4nCopy Citation Copied
URL: https://dx.doi.org/10.17504/protocols.io.ehjbb4n
Authors: Bonnie Hurwitz, Ken Youens-Clark
Group: VERVE Net, Hurwitz Lab
Summary: K-mer-based approaches to determining sequence similiarity can be faster than traditional use of BLAST. This application uses Jellyfish to index host FASTA files, then uses the mode value (default 2) of the number of matching k-mers (default k=20) from the input sequence to determine whether the sequence is similar enough to the host sequence to be rejected. The output of the app is:"screened" directory containing the sequences from each file that were found to be dissimlar to the host"rejected" directory containing the sequence from each file that were too similar to the host"jf" directory containing Jellyfish indexes of each "host" file (useful for later runs with other files to skip recreating)"kmer" directory containing k-mers of query sequences and ".loc" file showing the number of ".kmer" lines associated to each sequence Code is freely available at Github.
Affiliations: University of Arizona, University of Arizona
Version: 1
Publication Date: 2016
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Source: Protocols.io
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