
K-mer-based approaches to determining sequence similiarity can befaster than traditional use of BLAST. This application usesJellyfishto index host FASTA files, then uses the mode value (default 2)of the number of matching k-mers (default k=20) from the input sequenceto 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 atGithub.
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