Biological diversity in New Caledonia-Kanaky : Characterization from freshwater crustaceans, identification of major explicative factors and perpetuation of knowledges for their (re-)use

Original AB1 data files for these sequenced are shared along with tabular data files on individuals (containing e.g. sample ID, species and sex identified, NCBI GenBank accession for cleaned sequences and used primers for amplifications), occurences (containing e.g. sample ID, species identified, French Natural History Museum (MNHN) collection ID), samples (containing e.g. sample type, location ID, sampling date, sampler name), locations (containing e.g. other names of the location, coordinates in decimal degrees WGS84) and DNA extractions (containing e.g. extraction date, laboratory operator) and fasta files with all found haplotypes sequences and primer used.

DNA extraction (dx.doi.org/10.17504/protocols.io.j8nlk4x7wg5r/v1; dx.doi.org/10.17504/protocols.io.36wgqnm9ygk5/v1) and PCR (dx.doi.org/10.17504/protocols.io.261ge4y4jv47/v2; dx.doi.org/10.17504/protocols.io.n92ld8q57v5b/v1) protocols are available on protocols.io. Sequence cleaning workflow is available on Galaxy at usegalaxy.fr/u/coline_royaux/w/sanger1--from-ab1-to-aligned-fasta-imported-from-uploaded-file ; usegalaxy.fr/u/coline_royaux/w/sanger1--from-ab1-to-consensus-and-blast-no-final-alignment and history retracing data cleaning steps at usegalaxy.fr/u/coline_royaux/h/automatic-boeckella-nc-data-cleaning-1 ; usegalaxy.fr/u/coline_royaux/h/boeck-sanger-2024-clean.