BWA Support

The pipeline now supports BWA, for aligning reads to nucleotide bait sequences. While faster, it may reduce the specificity, if reads are unable to align to nucleotide baits due to high sequence divergence. The BLASTx pipeline is still the default, and may provide higher specificity.

First DOI Release

Many bugfixes have been made, most critically the bug which was adding each read twice for each gene, if both the forward and reverse reads had BLASTX hits. Several usability fixes were added, and more features for adjusting downstream parameters for Velvet and Exonerate.

Finally, a GPL v3 license was added to the repository in preparation for generating a DOI for this release.

Reads-First Capability

Adds the ability to start with the raw Illumina reads. Velvet, CAP3, and GNU Parallel are now required. Reads are distributed to separate files, one per target gene, based on BLASTx hit scores. If there are multiple baits per target gene, the best reference is chosen by highest cumulative BLASTx score.

Release 0.0.2

Added hybseq_summary.py, a helper script to describe the lengths of every gene as a result of the first two scripts.

Initial Release

Two main scripts:

query_file_builder.py Sets up file hierarchy and creates "tailored baits" file for each gene.
exonerate_hits.py Generates protein and nucleotide sequences (in frame) from exonerate hits to each gene.