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:
Nextera DNA Library Prep manual
For MinION:
MinION Genomic Ligation Sequencing Protocol
QC:
Bioanalyzer DNA High Sensitivity Manual
dnf-474-hs-ngs-fragment-analysis-kit-1bp-6000bp-user-manual
dnf-474-quick-start-guide-12-capillary-11-03-2015
A Guide to Looking at Bioanalyzer and Fragment Analysis Runs
Seq System_Coverage Calculator 2013 Aug19 (1)
Calculations And Conversions For Illumina Miseq Run
Jan2017SamplePreparationandperformingaRunonMiSeq.docx
Helpful Literature and CMB generated Bioinformatics Workflows
illumina-adapter-sequences-1000000002694-11
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
MinION
RNAseq
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
RNASeq Analysis using Rockhopper (for bacterial transcriptomes only)
16S Metagenomics
16s-metagenomic-library-prep-guide-15044223-b
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
Examining Global Distribution of dominant archaeal populations in soil – Article
Metagenomics Research Review – Article
Ultra-high-throughput microbial analysis on Illumina platforms
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