Arguing for khmer's impact, for an NIH R01 grant proposal

I'm starting to work on a grant renewal for khmer, and with a lot of help from the community, including most especially Richard Unna-Smith, I've put together the following blurb. Suggestions for things to rearrange, highlight or omit welcome, as well as suggestions for things to add. I can't make it too much longer, though.


The primary software product from previous funding is the khmer software. khmer provides reference implementations of low-memory probabilistic k-mer counting with the CountMin Sketch (pmid25062443), metagenome graph partitioning with probabilistic De Bruijn graphs (pmid 22847406), lossy compression of large sequencing data sets with digital normalization (arXiv), and streaming error trimming (PeerJ preprint).

Software details First made available in 2010, khmer now contains 12k lines of C++ code with a 6.6k-line Python wrapper library and test suite; khmer functionality is exposed at the C++ level, the Python level, and through the command line. We have intentionally chosen to maximize use and reuse by releasing the software early and often, making preprints available, and lowering barriers to reuse. In particular, we make khmer freely available for commercial and non-commercial use, reuse, modification, and redistribution under the BSD license. There are also no IP restrictions on the algorithms implemented in khmer, so companies have been able to make maximal use of the software; for example, Illumina directly incorporates the software in their synthetic long-read pipeline (pmid25188499}.

Development process and developer community Our development process adheres to many good practices, including version control, use of an issue tracker, maintaining high test coverage ($>$80%), coding and test guidelines, a formal code review and contribution process, and continuous integration (pubmed24415924, Crusoe and Brown). Our formal release process (link) tests the khmer software across multiple UNIX distributions prior to release, and we now have 25 releases. About 60 people have contributed patches to khmer, and there is an active core of 5 developers, including one external to our group. We have a low-traffic mailing list with 100 subscribers. The GitHub project has 237 "stars" and 192 forks, placing it in the top 1% of science projects on GitHub.

Documentation, protocols, and recipes We maintain documentation for command-line use (link), detailed protocols for integration with other software (link), and an increasing number of "recipes". With Google Analytics, we have seen approximately 10,000 distinct visitors to these sites within the last 15 months.

Software use khmer is widely used by external groups, is frequently downloaded, and has led to several extensions of the core algorithms first demonstrated in khmer. In particular, khmer is downloaded from the Python Package Index 2-3k times a month, and is available for install through several UNIX distributions. Because khmer is available from many different sites, these are most likely underestimates.

Citations In addition to three publications and N preprints from our group (link and citations), and four publications with collaborators (cite), a literature survey found 26 publications using the software in data analysis (link). Accurate numbers are hard to report because many papers do not cite computational tools properly, some journals do not allow preprint or Web site citations, and tool citations are often removed from high impact-factor citation lists for space reasons; however, searching Methods sections in open-access biomedical journals (approximately 20% of the literature) found 26 publications, so we estimate the true citation count at greater than 100. Moreover, several pipelines and workflow engines incorporate khmer, including Illumina TruSeq long reads (pubmed25188499), DOE KBase, iPlant Collaborative, and Galaxy, potentially leading to a deflated citation count.

Scientific usage khmer has been used for assembling highly heterozygous genomes, including a number of parasitic nematodes (e.g. (pmid25730766,24690220,23985341); microbiome analysis, including both environmental and human/host-associated (pmid25279917,pmid24632729); mRNAseq de novo assembly (pmid25758323,pmid24909751); and preprocessing for PacBio error correction and RNA scaffolding (cite). (See (lik) for a full list of citations.) Several groups doing large-scale genomics now incorporate khmer into their pipeline to dramatically reduce time and memory requirements for assembly; for example, the Hibberd Lab at Cambridge is using it to reanalyze over 240 deeply sequenced plant transcriptomes.

Extensions and reimplementations In addition to direct use of the khmer software, several groups have reimplemented and extended concepts first demonstrated in khmer. This includes the in silico normalization algorithm included in the Broad Institute's Trinity package for de novo mRNAseq assembly (pmid23845962); NeatFreq, another implementation of abundance normalization, released by JCVI (pmid25407910); bbnorm, developed at JGI (cite); and an implementation of diginorm in the Mira assembler. The Minia assembler (pmid24040893) extends the probabilistic De Bruijn graph approach first introduced in Pell et al., 2012, and this has been further extended for cascading Bloom filters (pmid24565280).

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