Paralog Warnings and New Name

Now with using the SPAdes assembler, there is a higher likelihood of assembling long contigs for each gene. If paralogs (or divergent alleles) exist for the gene sequence, SPAdes will generate multiple long-length contigs.

In this release, the pipeline will generate warnings if there are multiple long-length contigs for each gene in "paralog_warning.txt" within each gene file. It will also save a general "genes_with_paralog_warnings.txt" file in the main directory with a list of genes to consider further.

One option for paralogous genes is to extract coding sequences from each paralog and treat them as separate loci, and re-run the pipeline. The reads may then be accurately distributed to each paralog.

We are also happy to report the name change of the pipeline to HybPiper! Thanks to the Wickett Lab for help with the strenuous naming process. For now our logo is the following, by Elliot Gardner: