Ballini & Staffoni et al. (submitted to Hydrobiologia) workflow

Supporting codes for Manu et al., Ecological Indicators (2023). Deep sequencing of extracellular eDNA enables total biodiversity assessment of ecosystems

In this project a standardised AlphaFold 2-based molecular replacement strategy is developed and implemented in an existing biomolecule structure solution pipeline at MAX IV Laboratory. It can be run on high performance clusters similar to the LUNARC (https://www.lunarc.lu.se/). A standalone and implemented version of the pipeline exists.

TaxonTableTools - A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data

Written by Emily Curd (eecurd@g.ucla.edu), Jesse Gomer (jessegomer@gmail.com), Gaurav Kandlikar (gkandlikar@ucla.edu), Zack Gold (zjgold@ucla.edu), Max Ogden (max@maxogden.com), Lenore Pipes (lpipes@berkeley.edu)and Baochen Shi (biosbc@gmail.com). Assistance was provided by Rachel Meyer (rsmeyer@ucla.edu).

A snakemake workflow based on the obitools suite of programs, that analyzes DNA metabarcoding data.

This is the command line version of MiFish pipeline. It can also be used with any other eDNA meta-barcoding primers

Mitohelper: a mitochondrial reference sequence analysis tool for fish eDNA studies