Definition

khmer is an open source project that serves as:

• a stable research platform for novel CS/bio research on data structures and algorithms, mostly k-mer based;
• a set of of command line tools for various kinds of data transformations;
• a test bed for software engineering practice in science;
• a Python library for working with k-mers and graph structures;
• an exercise in community building in scientific software engineering;
• an effort to participate in and sustainably grow the bioinformatics ecosystem.

Goals

Our long term goals for khmer, in some rough order of priority, are:

• Keep khmer versatile and agile enough to easily enable the CS and bio we want to do.

  Practical implications: limit complexity of internals as much as possible.

• Continue community building.

  Practical implications: run khmer as a real open source project, with everything done in the open; work nicely with other projects.

• Build, sustain, and maintain a set of protocols and recipes around khmer.

  Practical implications: take workflow design into account.

• Improve the efficiency (time/memory) of khmer implementations.

  Practical implications: optimize, but not at expense of clean code.

  Some specifics: streaming; variable sized counters.

• Lower barriers to an increasing user base.

  Practical implications: find actual pain points, address if it’s easy or makes good sense.

  Some specifics: hash function k > 32, stranded hash function, integrate efficient k-mer cardinality counting, implement dynamically sized data structures.

• Keep khmer technologically up to date.

  Practical implications: transition to Python 3.

--titus

p.s. Thanks to Qingpeng Zhang, Travis Collier, and Matt MacManes for comments in the draft stage!