RFC: The khmer project: what are we, and what are our goals?

As we think about the next few years of khmer development, it is helpful to explore what khmer is, and what our goals for khmer development are. This can provide guiding principles for development, refactoring, extension, funding requests, and collaborations. Comments solicited! Links: khmer github repo: https://github.com/ged-lab/khmer/ khmer docs: http://khmer.readthedocs.org/ Definition khmer is an open …

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Estimate whether your sequencing has saturated your sample to a given coverage

This recipe provides a time-efficient way to determine whether you’ve saturated your sequencing depth, i.e. how much new information is likely to arrive with your next set of sequencing reads. It does so by using digital normalization to generate a “collector’s curve” of information collection. Uses for this recipe include evaluating whether or not you …

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Being a release manager for khmer

We just released khmer v1.1, a minor version update from khmer v1.0.1 (minor version update:220 commits, 370 files changed. Cancel that — _I_ just released khmer, because I’m the release manager for v1.1! As part of an effort to find holes in our documentation, “surface” any problematic assumptions we’re making, and generally increase the bus factor of the khmer project, …

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Announcing khmer 1.0

The khmer team is pleased to announce the release of khmer version 1.0. khmer is our software for working efficiently with fixed length DNA words, or k-mers, for research and work in computational biology. Links: khmer documentation PyPI link Announcement ChangeLog Citation handle khmer v1.0 is the culmination of about 9 months of development work …

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