Curated_reference_databases

This repository contains the complete description of how we produced the curated reference databases for the studies in Evolutionary and Environmental Genomics Group (@EvoHull)

Currently, we have completed the curated reference databases of mitochondrial 12S and Cytb including European freshwater fish, UK amphibians, UK birds, UK reptiles and UK mammals.

Contents

#The contributors for each database as below:

Cytb

• European freshwater fish by Christoph Hahn GitHub ID chrishah

12S

• European freshwater fish by Jianlong Li GitHub ID JoeJianlongLi and Christoph Hahn GitHub ID chrishah

• UK amphibians by Lynsey R. Harper GitHub ID lrharper1

• UK birds by Lynsey R. Harper GitHub ID lrharper1

• UK reptiles by Lynsey R. Harper GitHub ID lrharper1

• UK mammals by Lynsey R. Harper GitHub ID lrharper1

#Work your way through the notebooks in the individual directories in the following order with slightly changes between the databases:

• Convert_denovo_fasta_to_gb (If you do not have denovo fasta sequences, skip it)
• fetch-and-clean
• nr (We sometime combined fetch-and-clean and nr to fetch_clean_align or fetch_clean_align_tree)
• SATIVA
• post_SATIVA

Final clean database

You can find the final clean database which has been labeled by *SATIVA_cleaned*.gb (for example) in each database.

Setting up the environment

To facilitate full reproducibility of our analyses we provide Jupyter notebooks illustrating our workflow in this repository.

In the individual directory listed above of each database, you can find the Jupyter notebooks *.ipynb (for example) which you can use them for reproducible analysis.

You need the metaBEAT pipeline, which relies on a range of open bioinformatics tools, which we have wrapped up in a self contained docker image which includes all necessary dependencies here.

metaBEAT is using a number of external programs. To make your life easier we have created a self contained environment with all necessary pieces of software in a docker image. This image is building on ReproPhylo. If you want to use it you'll need Docker installed on your machine.

The more details about how to install the Docker and metaBEAT, please go to visit the GitHub repository in here.

Publications

#The publications have used the curated reference databases in this repository

• Hänfling, B., Lawson Handley, L., Read, D.S., ... Winfield, I.J. (2016) Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods. Molecular Ecology, 25, 3101-3119. (DOI) (GitHub)

• Harper, L.R., Lawson Handley, L., Hahn, C., ... Hänfling, B. (2018) Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt (Triturus cristatus). Ecology and Evolution, 8, 6330-6341. (DOI) (GitHub)

• Li, J., Lawson Handley, L.J., Read, D.S. & Hänfling, B. (2018) The effect of filtration method on the efficiency of environmental DNA capture and quantification via metabarcoding. Molecular Ecology Resources, 18, 1102-1114. (DOI) (GitHub)

• Sellers, G.S., Di Muri, C., Gomez, A. & Hänfling, B. (2018) Mu-DNA: a modular universal DNA extraction method adaptable for a wide range of sample types. Metabarcoding and Metagenomics, 2: e24556. (DOI) (OSF)

• Li, J., Hatton‐Ellis, T.W., Lawson Handley, L.J.,... Hänfling, B. (2019) Ground‐truthing of a fish‐based environmental DNA metabarcoding method for assessing the quality of lakes. Journal of Applied Ecology, 56, 1232–1244. (DOI) (GitHub)

• Lawson Handley, L.J., Read, D.S., Winfield, I.J., ... Hänfling, B. (2019) Temporal and spatial variation in distribution of fish environmental DNA in England’s largest lake. Environmental DNA, 1, 26-39. (DOI) (GitHub)

• Li, J., Lawson Handley, L.J., Harper, L.R.,... Hänfling, B. (2019) Limited dispersion and quick degradation of environmental DNA in fish ponds inferred by metabarcoding. Environmental DNA, 00, 1-13. (DOI) (GitHub)