Two numeric CSS counter styles are defined for Khmer, using Khmer digits, in the document Ready-made Counter Styles: khmer and cambodian. Both styles are exactly the same, and are listed separately because both names are supported in some browsers, and it makes it easier to cut and paste if two clean instances are provided.
The khmer-consonant style is not supported by any browser natively, and although the CSS Counter Styles spec allows users to create their own counter styles, the feature is only implemented by Firefox at the moment, so no support is available for this style.
Nhc Khmer
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khmer is both research software and a software product for users: it has been used in the development of novel data structures and algorithms, and it is also immediately useful for certain kinds of data analysis (discussed below). We continue to develop research extensions while maintaining existing functionality.
Memory requirements for using khmer vary with the complexity of data and are user configurable. Several core data structures can trade memory for false positives, and we have explored these details in several papers, most notably Pellet al. 20122 and Zhanget al. 20141. For example, most single organism mRNAseq data sets can be processed in under 16 GB of RAM3,8, while memory requirements for metagenome data sets may vary from dozens of gigabytes to terabytes of RAM.
The user interface for khmer is via the command line. The command line interface consists of approximately 25 Python scripts; they are documented at underUser Documentation. Changes to the interface are managed with semantic versioning9 which guarantees command line compatibility between releases with the same major version.
khmer development has largely been supported by AFRI Competitive Grant no. 2010-65205-20361 from the USDA NIFA, and is now funded by the National Human Genome Research Institute of the National Institutes of Health under Award Number R01HG007513, as well as by the the Gordon and Betty Moore Foundation under Award number GBMF4551, all to CTB.
The paper itself does a good job of describing the software at a high level, including the overall design and goals. I would have appreciated slightly more detail about the motivation behind the design decisions, and the tradeoffs they entail (e.g. Why have a Python front-end? Why use hand-written binding code rather than a binding generator, like SWIG, that would allow interfaces to other languages as well?). I understand that a comprehensive description is not feasible in a manuscript of this length. It would be very interesting to know, however, the cost paid for using the high-level interface rather than the C++ library directly. When the underlying computation is trivial, simply having to iterate over an enormous number of things in Python could add non-trivial overhead. Despite these desiderata, I find that the paper is generally well written and does a good job of describing what a new user might want to know about khmer, and so I approve of this manuscript.
This brings me to my final point, about the (currently) controversial authorship policy on this paper, which is ancillary to the quality of the paper (and software) itself. At this point,I must reserve judgement on whether I think the authorship policy adopted by this paper is "good" or "bad" (for science, the community, etc.). Incidentally, this is a dichotomy that does not capture the subtlety or importance of this issue well. In the manuscript, the authors state "We develop khmer on github.com as a community open source project focused on sustainable software development, and encourage contributions of any kind." Thus, contributions to khmer are of a potentially wide variety in character (and also, I believe, not simply related to improving or maintaining the code). Those who contribute to the design, improve the usability, work on documentation, support new and existing users, and develop and propagate best practices are all contributing something valuable to the khmer software "ecosystem". It is unreasonable to expect a piece of software that is ~25k lines of code (and growing) to be actively developed, maintained, and supported by only a small contingent of people, many of whom may be graduate students soon to graduate and move on. Thus, if we are interested in the long-term viability and quality of such software, we must adopt a system of credit that values and recognizes a variety of different types of contribution. On the other hand, I do share the concern that, in the midst of the current authorship system, bestowing that recognition in the form of authorship may have the adverse effect of diminishing the public perception of the very credit one is trying to grant. Perhaps there is a solution along the lines adopted by this paper, or perhaps something drastically different needs to be considered.
The khmer software is a set of command-line tools for working with DNAshotgun sequencing data from genomes, transcriptomes, metagenomes, andsingle cells. khmer can make de novo assemblies faster, andsometimes better. khmer can also identify (and fix) problems withshotgun data. You can read more about khmer in our software paper.
We have additional documentation in several places, includingprotocols for metagenome and mRNAseq assembly and recipes for severalcommon research tasks.You might also be interested in papers using or citing khmer.
khmer development was initially supported by AFRI Competitive Grantno. 2010-65205-20361 from the USDANIFA, and is now funded by the National Human Genome ResearchInstitute of the National Institutes of Health under Award NumberR01HG007513through May 2016, both to C. Titus Brown. More recently, we havereceived support from the Gordon and Betty Moore Foundation underAward number GBMF4551.
first point of contact when looking for help: -lab/khmer/issuesmailing list for discussion: mailing list for announcements: -announceemail contact for project maintainers:khmer-project@idyll.orgImportant note: cite us!khmer is research software, so you should cite us when you use it in scientific publications!Please see the CITATION file for citation information. e24fc04721
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