PURC
PURC, created by Carl and Fay-Wei Li, is a pipeline for inferring the underlying biological sequences (alleles, paralogs, or homeologs) from amplicon sequencing data (PacBio, Illumina, etc), de-multiplexing them (labeling each sequence with its locus and source sample), and cleaning them (removing PCR errors, sequencing errors, and chimeras). It is geared toward analyzing polyploid species complexes but is also effective for other applications; the final output of a full run includes an alignment for each locus with each homeolog or allele sequence in the amplicon data labeled with the source sample information and amount of coverage. More information is available at the PURC site, and in our paper describing the method.
Misc. Scripts
Under construction/in review/being contemplated.