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Southern California Coastal Water Research Project

Susie Theroux's starred repositories

ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Language:NextflowMIT169 146 332

woltka

Woltka: a versatile meta'omic data classifier

Language:PythonBSD-3-Clause68 9 77

lulu

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

Language:ShellLGPL-3.061 5 16

biovcnet.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

Language:HTMLMIT60 130

mixs

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

Language:PythonCC0-1.036 19 721

BOLDigger

A python package to query different databases of boldsystems.org

Language:PythonMIT29 2 37

docs

Language:PythonBSD-3-Clause21 14 186

apscale

Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data

Language:PythonMIT12 1 14

microDecon

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

Language:R1205

refdb

A reference database manager for R

Language:R11 2 4

WorkingDogs

Home repo for the Working Dogs pack of bioinformatics tools

Language:C#MIT900

BOLDigger-commandline

BOLDigger as a commandline tool

Language:PythonMIT8015

omics-data-management

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

GPL-3.07 1 6

apps_for_fieldwork

Compendium of smartphone applications for field biology

Language:HTMLMIT7 2 3

qiime2_ASVworkflow_v8

Language:R600

miqScoreShotgunPublic

Repo for public-facing shotgun MIQ score

Language:HTMLGPL-3.06 6 2

miop

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

gruinard_decon

An eDNA metabarcoding decontamination pipeline

Language:RMIT5 10

MGPrimerEval

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

Language:Jupyter NotebookGPL-3.03 2 2

tourmaline

Amplicon sequence processing workflow using QIIME 2 and Snakemake

Language:PythonBSD-3-Clause3 30

Gap_Analysis

Language:R2 10

doc-publishing-dna-derived-data

This guide shows how to publish DNA-derived spatiotemporal biodiversity data and make it discoverable through national and global biodiversity data discovery platforms. Based on experiences from Australia, Norway, Sweden, UNITE, and GBIF.

NOASSERTION2 15 153

eDNA-metabarcoding-intro

Language:Shell200

MBON-Protocols

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

2 10

ASCI

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

Language:R2 4 47

Filek_et_al._2022-diatom_microbiota

Language:HTMLGPL-3.01 10

CALeDNA

Analysis scripts using data from the CALeDNA consortium

Language:RGPL-3.0100

EcoIndicators

Language:R1 20

db-build-microeuks

Documentation to build databases for 18S tag-sequencing or metaT/G work

Language:Python1 10

GEISHA_phytoplankton

code for GEISHA functional group classification R package

Language:R100