Protist Ribosomal Reference database (PR2) - SSU rRNA gene database

This is an automatic pipeline for analysis of amplicon sequence data including 16S, 18S and ITS. It wraps QIIME commands and complements them with additional analysis where QIIME is not good at, such as combine multiple sequencing runs, OTU clustering and chimeric removal with UP ARSE, alignment filtering with Gblock, removing Chloroplast sequen…

Scripts for paper Vaulot et al. 2022

Shiny application to access metaPR2 database

NGS4ECOPROD - An easy-to-use conda environment and pipelines for metagenome sequence analysis

Nanopore sequencing-based Amplicon Pipeline: optimised for full-length, 16S and 18S mixed amplicon datasets, in a fast and computationally efficient manner, setup for use of 515Y/926R primers, but also compatible with other cross-domain primers.

An R Shiny application to identify cochineal genetic sequences for 12S rRNA, 18S rRNA, or COI.

Datasets and statistics code used for "Objective 1" for PhD Thesis

CryptoGenotyper is a tool that allows for subtyping the parasite, Cryptosporidium

A custom bioinformatic workflow for UPDX (Universal Parasite Detection assay) sequences analysis.