NGS Resources

Power Points

MiSeq RNA Seq and Analysis ppt by Louie Bierwert


Nucleic Acid and Library Prep Protocols

CWZ Mini Boiling RNA Preparation

CWZ Mini Boiling RNA Preparation BCH 390 version

Recommended Kits for Library Prep

For the MiSeq:

Guide to Index combinations

NEBNExt Ultra RNA manual

Guide to Index combinations

Nextera DNA Library Prep manual

For MinION:

MinION Genomic Ligation Sequencing Protocol


Bioanalyzer DNA High Sensitivity Manual



A Guide to Looking at Bioanalyzer and Fragment Analysis Runs


Seq System_Coverage Calculator 2013 Aug19 (1)

Calculations And Conversions For Illumina Miseq Run


Helpful Literature and CMB generated Bioinformatics Workflows




How to view the quality graphs and summary in BaseSpace – SequencingAnalysisViewer_UserGuide

MAUVE – Multiple Genome (or transcriptome) Alignment Tool – free download

Workflow DNA de novo assembly using Soap De Novo on Commandline

DNA de novo assembly using NGen on BaseSpace

Eukaryotic Genomics Assembly and Annotation on CommandLine Jellyfish, Quake, and MakerII

Eukaryote Annotation Review Article

Prokaryotic Genomics Assembly and Annotation using NextGene and RAST





Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

RNASeq Analysis Workflow using Commandline – Tutorial

RNA Seq MiSeq Data Analysis WorkFlow Using Galaxy Mason Account_by_Louie_and_Weam

RNA Seq Analysis workflow w:o reference – Article

Advanced RNA Seq Analysis Topics and Trouble-Shooting – Article

P and q values in RNA Seq

RNASeq Analysis using Rockhopper (for bacterial transcriptomes only)




16S Metagenomics


Workflow from sample to analyzed data – uses Qiime for analysis – Tutorial

High-Speed, Multiplexed 16S Microbial Sequencing on the MiSeq® System – Article

Qiime allows analysis of high-throughput community sequencing data – Article

Earth Microbiome Project

Examining Global Distribution of dominant archaeal populations in soil – Article

Metagenomics Research Review – Article

Ultra-high-throughput microbial analysis on Illumina platforms

Qiime Tutuorial

Sirois Final Thesis – Comparison of the Fecal Microbiota of Horses Before and After Treatment for Parasitic Helminths: Massively Parallel Sequencing of the V4 Region of the 16S Ribosomal RNA Gene

Bioinfomatics tools
Here is a quick guide to RNASeq tools (some specific to E. coli) –RNA-Seq data analysis tools overview

PATRIC – has a free suite of NGS analysis tools with storage space and tutorials for the most popular applications including de novo assembly.  Set up an account and check it out.

UniPro UGENE – has tuxedo suite set up for RNAseq and more. Easy to use.

Galaxy – Main page – hit “user” button and register and you are good to go.

DAVID – for functional annotation

MeV – Multi-Experiment Viewer – lots of stats and visualization tools – free download

– a quick guide to Making a heatmap of expression with MeV

Rockhopper – A free RNA Seq tool for bacteria studies offered by Wellesley College that assembles, aligns and gene counts your data and produces alignment, coverage, and expression results that can be viewed with IGV, as well as gene lists that can be further explored in databases such as BioCyc.

IGV at the Broad Institute – an Integrated Genomics Viewer free download and support

Qiime – Command line program for metagenomics analysis

Cytoscape – Network data integration, analysis, and visualization in a box – free download

MEGA – Molecular Evolutionary Genetic Analysis – free download

You are going to run into GO terms wherever you go.  Here is an article delineating where they come from and what they mean – Gene Ontology annotations what they mean and where they come from (1)

Links to Genome Browsers – these integrate a lot of tools for annotation and pathway placement.

BioCyc – database for everything else

Wormbase – database for nematodes

EcoCyc – database for E.coli K12

RegulonDB – Ecoli Wiki

GreenGenes – a 16S database and workbench