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CITATION
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Software Citation
-----------------
If you use the khmer software, you must cite:
Crusoe et al., The khmer software package: enabling efficient
sequence analysis. 2014. doi: 10.6084/m9.figshare.979190
If you use any of our published scientific methods, you should *also*
cite the relevant paper(s), as directed below.
Graph partitioning and/or compressible graph representation
-----------------------------------------------------------
The load-graph.py, partition-graph.py, find-knots.py, load-graph.py,
and partition-graph.py scripts are part of the compressible graph
representation and partitioning algorithms described in:
Pell J, Hintze A, Canino-Koning R, Howe A, Tiedje JM, Brown CT.
Proc Natl Acad Sci U S A. 2012 Aug 14;109(33):13272-7.
doi: 10.1073/pnas.1121464109.
PMID: 22847406
Digital normalization
----------------------
The normalize-by-median.py and count-median.py scripts are part of
the digital normalization algorithm, described in:
A Reference-Free Algorithm for Computational Normalization of
Shotgun Sequencing Data
Brown CT, Howe AC, Zhang Q, Pyrkosz AB, Brom TH
arXiv:1203.4802 [q-bio.GN]
http://arxiv.org/abs/1203.4802
K-mer counting
--------------
The abundance-dist.py, filter-abund.py, and load-into-counting.py scripts
implement the probabilistic k-mer counting described in:
These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure
Zhang Q, Pell J, Canino-Koning R, Howe AC, Brown CT.
arXiv:1309.2975 [q-bio.GN]
http://arxiv.org/abs/1309.2975