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Cell Ranger Page Cell Ranger is the command-line software for preprocessing raw sequence data from a 10X single cell sequencing experiment. The output from Cell Ranger os a ...
Project management and quality assurance for RNAseq projects Page Managing your RNAseq project and checking the quality of raw data are essential first steps in the analysis of any RNAseq experiment. The protocol below out...
Depositing RNAseq data to GEO Page This page will walk you through the steps to make your data publicly available so you can meet the requirements for manuscript submission and publication
RStudio Server Page How to access RStudio through your web browser
Metagenomics in the cloud Page This 4 hour workshop takes users through setting up their own cloud computer, intalling a Snakemake-based pipeline called Sunbeam for analysis of shotgun met...
Kallisto Page Kallisto is our first choice for aligning reads because it combines speed, accuracy, and the ability to leverage bootstraps for modeling technical variance
CHMI linux server Page CHMI maintains a custom configured compute server that runs Linux Ubuntu 18.04 LTS. This machine has two 6-core Intel Xeon E5-2643v4 CPUs (12 cores total), ...
Preparing microbiome data for deposit to microbiomeDB.org Page Instructions on how to prepare your raw sequence data and metadata mapping file for submission to microbiomeDB.org
analysis of 16S rRNA gene sequencing data Page Preparation of V4 region, 16S dual-indexed libraries for sequencing on an Illumina platform
QIIME2 workflow Page Using the Quantitative Insights Into Microbial Ecology (QIIME2) software pipeline for analysis of marker gene-based microbiome sequencing data
Bioinformatics Software Page A summary of the bioinformatics software currently installed on our Linux cluster.
Exploring WGS and Metagenomic data using minHash sketches Page QC and analysis of microbial WGS and metagenomic data using Sourmash