Copyright © 2008, CMB Smith College
Nucleic Acid and Library Prep Protocols
Recommended Kits for Library Prep
New England Biolabs Carries Illumina compatible DNA and RNA library prep kits and Index kits with pricing
comparable to Illumina. In addition, they will give you an educational discount if using for a class. They just
recently released a magnetic bead kit for mRNA isolation from whole RNA. For most bacterial RNA applications,
you will want to eliminate rRNA. We recommend RiboZero by EpiBio for this step. For Sequencing ends-
NEB may come out with one but for right now it is Illumina's nextera_mate_pair_sample_prep_guide
The CMB is here to help with any questions you may have about making these selections.
Just contact Louie at email@example.com
Helpful Literature and CMB generated Bioinformatics Workflows
NGS Overview and Practical Approach to Variant Detection in NGS Data - Video. Need to download WebEx Viewer to View
RNASeq Analysis Without Reference - Article
Links to Bioinfomatics tools
Got a question? Try asking at SeqAnswers - The Next Generation Community -It's easy to join.
DNAStar Lasergene 11- Available to use on BaseSpace but it has to be on the computer
you are using in order to view results. Google DNAStar to see all of it's capabilities.
We currently have a network license, which means we can put on any Smith computer
but only 4 can be in use at one time,so be sure you quit when you are done.
Lasergene 11 is loaded onto the AppleCart computers in the CMB - please be sure to
sign out the AppleCart if you need a computer for this purpose. Thanks
CLC Genomics Workbench - Can sign up for a 6 month free trial for having the MiSeq
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
Cytoscape - Network data integration, analysis, and visualization in a box
MEGA - Molecular Evolutionary Genetic Analysis
IGV at the Broad Institute - an Integrated Genomics Viewer
Qiime - Command line program for metagenomics analysis
Links to Genome Browsers
Ecocyc - database for E.coli K12
RegulonDB - Ecoli Wiki
GreenGenes - a 16S database and workbench
IF YOU WOULD LIKE TO ADD A LINK, PAPER OR PROTOCOL TO THIS SITE, OR IF THERE IS SOMETHING MORE YOU WOULD
LIKE TO SEE ADDED TO THIS PAGE, PLEASE CONTACT LOUIE BIERWERT AT firstname.lastname@example.org THANKS