SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
New Resources for 1000 Genomes laura Bioinformatics 36 04-15-2017 08:48 AM
Resources for miRNA Expression koneru_18 Bioinformatics 3 10-15-2013 05:05 AM
Bioconductor R Tutorials / Help for Beginners ETHANol Bioinformatics 11 10-29-2012 07:07 PM
Sequence resources kevotu General 4 11-07-2011 06:48 AM
CoComputational Resources on Assembling Genomes raghavagps Bioinformatics 0 01-17-2010 09:56 AM

Reply
 
Thread Tools
Old 06-02-2011, 09:35 AM   #1
MikeyG
Junior Member
 
Location: Colorado

Join Date: Jun 2011
Posts: 4
Default Recommended resources for beginners?

Hi all,

I am a novice "nextgen sequencer". My background is in biophysics/protein crystallography, and I have just embarked upon a postdoc in systems biology (big jump). I'm wondering if any folks can direct me to some good entry-level/intermediate nextgen sequencing reading material (books, journal articles, websites, etc), that may bring me up to speed - or nearly up to speed - on the fundamentals of these technologies. I will primarily be utilizing Illumina and 454, if this helps narrow things down.

Thanks so much for your help!
Mike
MikeyG is offline   Reply With Quote
Old 06-02-2011, 03:42 PM   #2
Kennels
Senior Member
 
Location: Sydney

Join Date: Feb 2011
Posts: 149
Default

Hello

Galaxy (http://main.g2.bx.psu.edu/) has some tutorials on analyses

Somewhat outdated but still very relevant is this thread:
http://seqanswers.com/forums/showthread.php?t=43

Google 'next generation sequence reviews" and you should pick up some material from there

If you go to the company's websites they have their own relevant publications too

good luck
Kennels is offline   Reply With Quote
Old 06-02-2011, 04:01 PM   #3
ECO
--Site Admin--
 
Location: SF Bay Area, CA, USA

Join Date: Oct 2007
Posts: 1,358
Default

Here are some:

General technology summaries: http://seqanswers.com/index.php?pageid=summaries

...I put some in my slides in this thread (http://seqanswers.com/forums/showthread.php?t=11597)

Also for software tools please don't miss the wiki: http://wiki.seqanswers.com

Welcome!
ECO is offline   Reply With Quote
Old 06-05-2011, 01:43 AM   #4
helwr
Junior Member
 
Location: United States

Join Date: May 2011
Posts: 1
Default

these papers on High Throughput Sequencing are pretty good: http://www.cs.columbia.edu/~itsik/SeminarSequencing.htm also see http://www.quora.com/Computational-G...ional-genomics
helwr is offline   Reply With Quote
Old 06-14-2011, 10:42 PM   #5
Jose Blanca
Member
 
Location: Valencia, Spain

Join Date: Aug 2009
Posts: 70
Default

We also have som documentation for our students: http://bioinf.comav.upv.es/courses/sequence_analysis/
Jose Blanca is offline   Reply With Quote
Old 06-14-2011, 11:21 PM   #6
ulz_peter
Senior Member
 
Location: Graz, Austria

Join Date: Feb 2010
Posts: 219
Default

Actually you have already found the most valuable website regarding NGS:

This one.
ulz_peter is offline   Reply With Quote
Old 06-17-2011, 05:13 PM   #7
robs
Senior Member
 
Location: San Diego, CA

Join Date: May 2010
Posts: 116
Default

Data preprocessing:
http://prinseq.sourceforge.net/manual.html#QC

Read mapping/aligning:
http://lh3lh3.users.sourceforge.net/NGSalign.shtml
http://lh3lh3.users.sourceforge.net/practical.shtml
http://bib.oxfordjournals.org/conten...bq015.abstract
robs is offline   Reply With Quote
Old 03-02-2012, 05:05 AM   #8
gormleymp
Member
 
Location: Philadelphia

Join Date: Feb 2012
Posts: 19
Default

I am a bioinformatician new to the field of NGS. My training to this point has been in the analysis of gene and protein expression data. I am looking for recommended resources for an introduction to NGS and catching up to the field. I saw this thread and thought I would revive the discussion. I will certainly check out these links. Any new recommendations?

Thanks for your help.
gormleymp is offline   Reply With Quote
Old 03-02-2012, 05:34 AM   #9
JackieBadger
Senior Member
 
Location: Halifax, Nova Scotia

Join Date: Mar 2009
Posts: 381
Default

user friendly programs:

recall your bases with PyroBayes http://bioinformatics.bc.edu/marthlab/PyroBayes

Assess basic characteristics and filter on quality with Prinseq http://edwards.sdsu.edu/prinseq_beta/

sort amplicons (if applicable), usin jMHC http://code.google.com/p/jmhc/
JackieBadger is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:41 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO