meancure 1.2.0

Metabarcoding Analysis with a Custom Reference

MEtabarcoding-ANalysis against a CUstom REference (MEAN-CURE)

Introduction

This script is used for the Analysis of Metabarcoding results from the Apscale Pipeline from a custom reference database. It assignes taxonomic information to the ESV sequences and can check the plausibility of these assignments by querying GBIF occurrence records.

BLAST search

Performs a BLAST search of ESV sequences against a custom reference database (see Requirements for details). The maximum number of BLAST hits to keep can be set in the settings file. It also incorporates information about the length of the query coverage, which is used in the analysis step.

Analysis

Filters the BLAST hits, so that the top 3% of the most identical records remain as candidates. These results are then calculated into a BLAST score.

GBIF occurrence search

The resulting analysed esv tabel can further be checked against occurrence records on GBIF. The settings file allows the creation of a circle (point and radius) in which occurrences should be present. Cutoffs for the year since when occurrences are counted and the minimum number of occurrences can be set. The best blast hits (family, genus and species level) from the results file will be labeled as plausible or implausible depending on occurrences in the set parameters. Entries from the other_candidates column will only appear, if they are likely to occur according to GBIF.