=======================================
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://angus.ged.msu.edu.s3.amazonaws.com/88m-reads.fa.gz

The `filter-exact <http://github.com/ctb/khmer/blob/master/scripts/filter-exact.py>`__ script can be used as a starting point.

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
<http://github.com/ctb/khmer/blob/master/scripts/fasta-to-abundance-hist.py>`__
and `abundance-hist-by-position
<http://github.com/ctb/khmer/blob/master/scripts/abundance-hist-by-position.py>`__
scripts can be used to generate the k-mer abundance profile data::

  %% python scripts/fasta-to-abundance-hist.py <filename> <K>
  %% python scripts/abundance-hist-by-position.py <filename>.<K>.hist > out

e.g.::

  %% python scripts/fasta-to-abundance-hist.py 88m-reads.fa 17
  %% python scripts/abundance-hist-by-position.py 88m-reads.fa.17.hist > 17.txt

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.

The quality trimming script is in `scripts/quality-trim.py <http://github.com/ctb/khmer/blob/master/scripts/quality-filter.py>`__::

  %% python scripts/quality-trim.py <fastq file> <trimmed file>

You can assess high/low abundance k-mer distributions with the
`hi-lo-abundance-by-position script <http://github.com/ctb/khmer/blob/master/scripts/hi-lo-abundance-by-position.py>`__::

  %% python scripts/hi-lo-abundance-by-position.py <fasta file>

This will produce two output files, <filename>.pos.abund=1 and
<filename>.pos.abund=255.