BOL: Next Generation Sequencing (NGS) Tutorials

Next Generation Sequencing (NGS) Tutorials

Jitendra Narayan — Sat, 24 Aug 2013 06:01:37 -0500

Institute of computational biomedicine, Cornell University provide an NGS workshop tutorial at http://chagall.med.cornell.edu/NGScourse/

You can also add your favourite NGS educational material, or workshop tutorial by commenting on this bookmarks for user benefit.

Understanding the basics of genome sequencing:

Tutorial by Luke Jostins.

http://www.genetic-inference.co.uk/blog/2009/04/basics-sequencing-dna-part-1/

http://www.genetic-inference.co.uk/blog/2009/08/basics-sequencing-dna-part-2/

A window into third-generation sequencing

http://hmg.oxfordjournals.org/content/19/R2/R227.full.pdf

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NGS data analysis pipelines

Detecting and annotating genetic variations using the HugeSeq pipeline DOI: 10.1038/nbt.2134
NARWHAL, a primary analysis pipeline for NGS data http://bioinformatics.oxfordjournals.org/cgi/content/abstract/28/2/284?etoc
RseqFlow: Workflows for RNA-Seq data analysis DOI: 10.1093/bioinformatics/btr441
ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence 10.1186/1471-2164-12-285
A framework for variation discovery and genotyping using next-generation DNA sequencing data PubMed: 21478889
SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects DOI: 10.1186/1471-2105-12-134 Abstract: http://www.biomedcentral.com/1471-2105/12/134/abstract
WEP: a high-performance analysis pipeline for whole-exome data http://www.biomedcentral.com/1471-2105/14/S7/S11
DDBJ read annotation pipeline: a cloud computing-based pipeline for high-throughput analysis of next-generation sequencing data. http://www.ncbi.nlm.nih.gov/pubmed/23657089
GATK: a Toolkit for Genome Analysis http://www.broadinstitute.org/gatk/
Metagenomics:http://www.nbic.nl/education/nbic-phd-school/course-schedule/ngsmetagenomics/
RNASeq:http://www.nbic.nl/education/nbic-phd-school/course-schedule/ngsrnaseq/
Bioinformatics and Seq courses: http://www.isb-sib.ch/training/training-activities-schedule/archive-2013.html
Variant Detection (Model organism) Advanced tutorial https://docs.google.com/document/pub?id=1CuKkKylVDb03tnN7RSWl5EUzleetn0ctjmvaidPKLxM
Variant Detection Introductory tutorial https://docs.google.com/document/pub?id=1ZRzrjjOCvtAu3m-IKL-rbJ1f4On60dDL_IEwG7oejdI
Microbial de novo Assembly for Illumina Data Introductory tutorial https://docs.google.com/document/pub?id=1N3AB9ptISUu4zULqe1kXpVF0BDyGb5f5yzxWSJd_WNM
RNAseq Differential Gene Expression Introductory tutorial https://docs.google.com/document/pub?id=1KbTiBHtvHLfPRZ39AY3uriazrINA8TJzgjjwn1zPP7Y

" Please add your favourite NGS link below in comment section for the benefit of bioinformatics community ".

Address of the bookmark: http://chagall.med.cornell.edu/NGScourse/

Comment by Manshi Raghubanshi

Manshi Raghubanshi — Sun, 25 Aug 2013 04:24:36 -0500

My favourite tutorial page for NGS based data analysis http://www.csc.fi/english/csc/courses/archive/ngs_workshop

Comment by Jitendra Narayan

Jitendra Narayan — Sun, 25 Aug 2013 04:20:49 -0500

If you use python for NGS data anaysis this page is will very informative for you:

https://extras.csc.fi/biosciences/courses/ngs/htseq/HTSeq_tour.pdf

http://www-huber.embl.de/users/anders/HTSeq/doc/tour.html

Comment by Rahul Agarwal

Rahul Agarwal — Sat, 24 Aug 2013 16:13:19 -0500

Another good resource:

http://bioinformatics.ca/workshops/2012/informatics-high-throughput-sequencing-data#outline

Comment by Poonam Mahapatra

Poonam Mahapatra — Sat, 24 Aug 2013 11:53:04 -0500

University of texas provide an excellent tutorial on NSG and Bioinformatics : https://wikis.utexas.edu/display/bioiteam/SSC+Intro+to+NGS+Bioinformatics+Course

Comment by Jitendra Narayan

Jitendra Narayan — Sat, 24 Aug 2013 06:16:48 -0500

The Cranfield University bioinformatics e-learning program provide an excellent NGS recources. This CUBELP web site is a platform for the pratical E-learning of Bioinformatics, principally, Next Generation Sequencing. The web site content includes a set of core public practical tutorials using case study examples to provide comprehensive training for Next Generation Sequencing data processing and analysis.

Find tutorial at http://elvis.ccc.cranfield.ac.uk/CUBELP2/faces/index.xhtml

Comment by Abhimanyu Singh

Abhimanyu Singh — Sat, 24 Aug 2013 06:09:04 -0500

I found this tutorial "Introduction to the analysis of next generation sequencing data" from Auckland University very informative.

Link : http://www.bioinformatics.auckland.ac.nz/workshops/NGS-workshop-update.pdf

In addition A Hitchhiker’s Guide to Next Generation Sequencing also very informative.

http://blog.goldenhelix.com/?p=423

http://blog.goldenhelix.com/?p=490

http://blog.goldenhelix.com/?p=510