HybPiper Manuscript Submitted

This is the version of HybPiper used to generate the analysis described in our manuscript:

HybPiper: extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment.

A number of improvements have been made since the last release:

Fixed a number of issues regarding selection of multiple full-length contigs.
--When two or more contigs are more than 85% of the length of the target reference, HybPiper will choose the contig with the highest coverage depth if it exceeds the next highest coverage depth by 10x. If not, percent-identity between the contig and target (at the amino acid level) is used as the criterion.
--Both the 85% length cutoff (--length_cutoff) and the 10x threshold (--depth_multiplier) can be changed by the user.

Fixed not using SPAdes properly for single-ended reads, should now use --s for single-end and --12 for paired-end

Added work-around for SPAdes assembly failures
--HybPiper will now re-do any failed SPAdes assemblies (where no contigs are generated).
--The highest-attempted k-mer value is removed, unless there is only one, in which case it is marked as a "dud"
--SPAdes can still produce contigs.fasta files of zero size, these are now recognized as failed assemblies.