.. This file is part of khmer, https://github.com/dib-lab/khmer/, and is Copyright (C) 2010-2015 Michigan State University Copyright (C) 2015-2016 The Regents of the University of California. It is licensed under the three-clause BSD license; see LICENSE. Contact: khmer-project@idyll.org Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the Michigan State University nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Contact: khmer-project@idyll.org ======================================= Blog posts and additional documentation ======================================= Hashtable and filtering ======================= The basic inexact-matching approach used by the hashtable code is described in this blog post: http://ivory.idyll.org/blog/jul-10/kmer-filtering A test data set (soil metagenomics, 88m reads, 10gb) is here: http://ci.oxli.org/userContent/88m-reads.fa.gz Illumina read abundance profiles ================================ khmer can be used to look at systematic variations in k-mer statistics across Illumina reads; see, for example, this blog post: http://ivory.idyll.org/blog/jul-10/illumina-read-phenomenology The `fasta-to-abundance-hist `__ and `abundance-hist-by-position `__ scripts can be used to generate the k-mer abundance profile data, after loading all the k-mer counts into a .ct file:: # first, load all the k-mer counts: load-into-counting.py -k 20 -x 1e7 25k.ct data/25k.fq.gz # then, build the '.freq' file that contains all of the counts by position python sandbox/fasta-to-abundance-hist.py 25k.ct data/25k.fq.gz # sum across positions. python sandbox/abundance-hist-by-position.py data/25k.fq.gz.freq > out.dist The hashtable method 'dump_kmers_by_abundance' can be used to dump high abundance k-mers, but we don't have a script handy to do that yet. You can assess high/low abundance k-mer distributions with the `hi-lo-abundance-by-position script `__:: load-into-counting.py -k 20 25k.ct data/25k.fq.gz python sandbox/hi-lo-abundance-by-position.py 25k.ct data/25k.fq.gz This will produce two output files, .pos.abund=1 and .pos.abund=255. Finding valleys/minima in *k*-mer abundance profiles ==================================================== Using *k*-mer abundance profiles to dynamically calculate the abundance threshold separating erroneous *k*-mers from real *k*-mers is described in this blog post: https://bitsandbugs.org/2016/07/29/mash-and-khmer-abundance/