Gene-level metagenomic analysis via de novo assembly

This release includes a significant change in the operation of the GeneShot analysis tool.

For a full summary of the behavior of the tool as represented in this release, please read the wiki associated with this repository.

This version is being pinned at v0.2.0 in anticipation of minor bugfixes which may be added, as well as potential added functionality. We plan to make a v1.0.0 release to accompany a publication of this tool, and we do not anticipate that the invocation of the tool will change at all by that point. At most, we may see additional output files generated with those minor revisions.

Alignment-based metagenomic sequence analysis

Geneshot v0.1.0 performs alignment-based quantification of microbial genes from whole-genome shotgun (WGS) sequencing data. Alignment is performed with DIAMOND, alignments are filtered with FAMLI, and the resulting abundance information is returned to the user in the form of HDF5 and CSV formatted files.