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amplicon-pacbio

PacBio ITS amplicon data

amplicon-pipelines-hpcc

ITS and 16S bioinformatic pipiliens to run on HPCC at Michigan State University

bacflux

A workflow for bacterial short reads assembly, QC, annotation, and more.

bash-for-bioinformatics

Usefull bash script and tricks to play with sequences

bioconda-recipes

Conda recipes for the bioconda channel.

blast-work-tools

cecilia

usearCh basEd ampliCon pIpeLine for Illumina dAta

constaxv2

dadaprep

Prepare your illumina reads before DADA2 pipeline

data-hygiene

demultiplex-usearch

Short pipeline to quickly demultiplex illumina amplicon data

gaap-bi

Genome Assembly and Annotation Pipeline for Bacteria Illumina

gaap-bp

Genome Assembly and Annotation Pipeline for Bacteria Pacbio

genome-work

git-resources

how-to-ggplot2

intro-to-rnaseq-hpc-o2

This repository has teaching materials for a 2 and 3-day Introduction to RNA-sequencing data analysis workshop using the O2 Cluster

metagaap

metaGenome Assembly and Annotation Pipeline

metagenome-work

misfunk

Miscellaneous R functions

nextflow-tutorial

playing-with-python

Python code for Bioinformatics

r-programming

rcode-for-microbiome

Scripts for analyzing microbiome data

scientific-papers-r-code

sra-database

Working with the Sequence Read Archive

students_modules_plp847

Student repo bioinfo code, homework and assignments

taganalysis

Repo for 16S and ITS workflows