v2.3.0

This version introduces the option to provide single ended reads to StrainR. To do this, PreProcessR must be run with --singleend, then StrainR may use the resulting database and be run when only provided one set of reads.

In addition, output files now include information about the percentage of k-mers that are unique.

v2.2.1

There is now background read correction available for the StrainR command, which is accessible through -b1 and -b2. These options allow the user to supply background reads which they wish not to be included in the final analysis. This is not a typical use-case.

For example, one could have an defined synthetic community with a background of an undefined community. To find the abundance of the defined community, supply reads as normal but also separately include background reads of just the undefined community to the -b1 and -b2 options. (e.g. the background reads could be day 0 of a mouse experiment before inoculation of a defined community.)

v2.1.0

This version includes some bug fixes, changes the naming scheme of subcontigs, adds unit testing, and adds the src and tests directories.

v2.0.0

This release introduces weighted percentile FUKMs (with number of unique k-mers as the weight) as an improved measure of strain abundances. In addition, hashcounter has been rewritten from python to C for major gains in speed and memory usage, making StrainR2 more accessible for use on personal computers.

v1.0.1

1.0.1 introduces various bug fixes to make StrainR2 less likely to throw an error on some inputs.

StrainR2v1.0.0

Initial Release