zanderiam/fishlib-africa

# Fish-Lib-Africa: A generalised, dynamic DNA reference library for metabarcoding of African freshwater fishes Based the original meta-fish-lib pipeline developed by: Collins, R.A., Trauzzi, G., Maltby, K.M., Gibson, T.I., Ratcliffe, F.C., Hallam, J., Rainbird, S., Maclaine, J., Henderson, P.A., Sims, D.W., Mariani, S. & Genner, M.J. (2021). Meta-Fish-Lib: A generalised, dynamic DNA reference library pipeline for metabarcoding of fishes. _Journal of Fish Biology_. doi.org. This repository hosts a comprehensive multi-locus mitochondrial DNA reference library dataset for freshwater fish species of Africa, derived from the NCBI GenBank and Barcode of Life BOLD databases. The dataset includes freshwater species, and can be employed in a variety of applications. Both native and introduced African freshwater fish species are included. A species coverage report for all primer sets can be found at assets/reports-tables.md. This African reference library is curated and ready-to-use, but the code provided here can easily generate a new reference library for a different location (see FAQ). In addition to providing quality controlled and curated fish references, this reference library has several unique features that make it useful to the wider DNA barcoding and DNA metabarcoding communities: * Flexible - the library is not limited to any particular metabarcode locus or primer set. I have included the most popular ones (Table 1), but new ones can be added as required. * Comprehensive - seaching by single gene names can often miss critical results due to poorly annotated records, but using hidden Markov models it is simple to extract homologous DNA fragments from large dumps of sequence data. * Exhaustive - searching by species names can exclude potential hits because of changes in taxonomy, but here we search for all species synonyms, and then subsequently validate those names to provide a taxonomically up-to-date reference library. * Reliable - …