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16s-rdna-dada2-pipeline

dada2 Nextflow pipeline

16s-rdna-pipeline

This repository contains an older version of our 16S rDNA diversity analysis pipeline. It uses a combination of bash scripts. To get a more updated version of the pipeline using Nextflow please go here: https://github.com/h3abionet/h3abionet16S/tree/master/workflows-nxf

16srrna-hex-tutorial

16S rRNA upstream and dowstream analysis tutorial for the UCT Hex cluster.

amptk

AMPtk: Amplicon ToolKit for NGS data (formally UFITS)

amw

16S analysis tutorial - part of Analysing the Microbiome Workshop 2017. We ran this on the Wits cluster.

bookdown

Authoring Books and Technical Documents with R Markdown

bugbase_manuscript

burrito

A visualization tool for exploratory data analysis of metagenomic data

decontamination

This script show how to decontaminate biological sequences from contaminant OTUs

h3abionet16s

H3ABioNet 16S package

h3agwas

GWAS Pipeline for H3Africa

hello_world

Just a first repository

kilaza

Config files for my GitHub profile.

metawrap

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

microbiome-analysis

IBRO-UCT

microbiome_helper

An assortment of scripts to help process and automate various microbiome and metagenomic bioinformatic tools.

microbiome_procedures

Mothur procedures for 16S and ITS analysis

midas

An integrated pipeline for estimating strain-level genomic variation from metagenomic data

miga

MiGA: Microbial Genomes Atlas

mothur

Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Immunology at The University of Michigan. This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.

newingit

git tutorial

phinch

Phinch is an open-source framework for visualizing biological data, funded by a grant from the Alfred P. Sloan foundation. This project represents an interdisciplinary collaboration between Pitch Interactive, a data visualization studio in Oakland, CA, and biological researchers at UC Riverside.

phyloseq-tools

pipits

Automated pipeline for analyses of fungal ITS from the Illumina

protocols

Our laboratory repository

python-novice-gapminder

Introduction to Python for non-programmers using gapminder data

strep-wgs-pbp-pipeline

Strep pneumoniae whole genome sequencing pipeline. The code in this repos was developed by Katie. It was done for a special request from the Medical Microbiology lab. Gerrit just moved it over from the original BitBucket space.

sunbeam

A robust, extensible metagenomics pipeline

training-material

A collection of Galaxy-related training material

trimmomatic

Read trimming tool for Illumina NGS data.