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Old 06-02-2011, 10:35 AM   #1
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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!
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Old 06-02-2011, 04:42 PM   #2
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Galaxy ( has some tutorials on analyses

Somewhat outdated but still very relevant is this thread:

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
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Old 06-02-2011, 05:01 PM   #3
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Here are some:

General technology summaries:

...I put some in my slides in this thread (

Also for software tools please don't miss the wiki:

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Old 06-05-2011, 02:43 AM   #4
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these papers on High Throughput Sequencing are pretty good: also see
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Old 06-14-2011, 11:42 PM   #5
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We also have som documentation for our students:
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Old 06-15-2011, 12:21 AM   #6
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Actually you have already found the most valuable website regarding NGS:

This one.
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Old 06-17-2011, 06:13 PM   #7
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Data preprocessing:

Read mapping/aligning:
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Old 03-02-2012, 06:05 AM   #8
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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.
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Old 03-02-2012, 06:34 AM   #9
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user friendly programs:

recall your bases with PyroBayes

Assess basic characteristics and filter on quality with Prinseq

sort amplicons (if applicable), usin jMHC
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