stheroux

meta-fish-lib

A generalised, dynamic DNA reference library for metabarcoding of fishes

meta-fish-pipe

Bioinformatics pipeline for fish metabarcoding

MBAcolors

Files associated with the MBAcolors package

mixs

Minimum Information about any (X) Sequence” (MIxS) specification

Gap_Analysis

microDecon

An R package for removing contamination from metabarcoding (e.g., microbiome) datasets post-sequencing

eDNA-metabarcoding-intro

MGPrimerEval

This is a snakemake pipeline that determines primer mismatches to SSU rRNA in metagenomic data.

BOLDigger

A python package to query different databases of boldsystems.org

BOLDigger-commandline

BOLDigger as a commandline tool

omics-data-management

Previous guide to omics data management, including NOAA Omics Data Management Plan.

Filek_et_al._2022-diatom_microbiota

ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2

miqScoreShotgunPublic

Repo for public-facing shotgun MIQ score

refdb

A reference database manager for R

qiime2_ASVworkflow_v8

apps_for_fieldwork

Compendium of smartphone applications for field biology

EcoIndicators

miop

A repository to store terms from the Minimal Information about an Omics Protocol specification

apscale

Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data

woltka

Woltka: a versatile meta'omic data classifier

MBON-Protocols

In lab and out of lab protocols for MBON eDNA collection and processing

lulu

r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)

docs

gruinard_decon

An eDNA metabarcoding decontamination pipeline

ASCI

R package for calculating Algal Stream Condition Index (ASCI) scores

GEISHA_phytoplankton

code for GEISHA functional group classification R package

CALeDNA

Analysis scripts using data from the CALeDNA consortium

WorkingDogs

Home repo for the Working Dogs pack of bioinformatics tools

tourmaline

Amplicon sequence processing workflow using QIIME 2 and Snakemake