Next Generation Sequencing (NGS)
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Next Generation Sequencing (NGS) Tutorials
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 ".
Comments
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
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
University of texas provide an excellent tutorial on NSG and Bioinformatics : https://wikis.utexas.edu/display/bioiteam/SSC+Intro+to+NGS+Bioinformatics+Course
Another good resource:
http://bioinformatics.ca/workshops/2012/informatics-high-throughput-sequencing-data#outline
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
My favourite tutorial page for NGS based data analysis http://www.csc.fi/english/csc/courses/archive/ngs_workshop
ANGUS is a site built around the 2010 course on Analyzing Next-Generation Sequencing Data. It contains a number of detailed tutorials on mapping, assembly, mRNAseq, ChIP-seq, and resequencing analysis. Enjoy!
http://ged.msu.edu/angus/index.html
Challenges and Solutions in the Analysis of Next Generation Sequence Data
http://lh3lh3.users.sourceforge.net/download/sam-20100630.pdf
Samtools & Gbrowse2 for NGS tutorial http://gorgonzola.cshl.edu/pfb/2010/LectureNotes/ngs2/ngs2.pdf
Link to recent developments and research papers on NGS algorithms https://www2.informatik.hu-berlin.de/~hakenber/links/nextgen.html
GeneSifter: Next Generation Data Management and Analysis for Next Generation Sequencing http://www.geospiza.com/Products/WhitePaper_06102009.pdf
Next generation sequencing tutorial by illumina http://res.illumina.com/documents/products/illumina_sequencing_introduction.pdf
A survey of tools for variant analysis of next-generation genome sequencing data http://bib.oxfordjournals.org/content/early/2013/01/21/bib.bbs086.full
Next-Generation Sequencing Workshop Materials
http://www.broadinstitute.org/science/programs/medical-and-population-genetics/next-generation-sequencing-workshop-materials
NGS tutorial http://lpm.hms.harvard.edu/palaver/sites/default/files/11_02_28_Dennis_Wall_1.pdf
Educational resources and tutorials on NGS can also be found at following websites:
https://www.vlsci.org.au/educational_resources_genomics
http://ged.msu.edu/angus/tutorials-2013/
NGSUtils is a suite of software tools for working with next-generation sequencing datasets. Links http://ngsutils.org/
http://omictools.com/ an useful tools for omics data analysis ...
Bioinformatics algorithms at
www.users-birc.au.dk/cstorm/students/Vesterstroem_Mar2006.pdf
www.proteomics.bioengr.uic.edu/people/ezra/cv/thesis_uic.pdf
NGS tutorial at http://www.bioinformatics.auckland.ac.nz/workshops/NGS-workshop-update.pdf
NGS tutorial for novice http://www.uni-mainz.de/FB/Biologie/Anthropologie/487_ENG_HTML.php
NGS related research paper on Bioinformatics Journal @ http://www.oxfordjournals.org/our_journals/bioinformatics/nextgenerationsequencing.html
Next Generation Sequencing for DUMMIES http://users.ugent.be/~avierstr/nextgen/Next_generation_sequencing_web.pdf
NGS tutorial http://www.bioinformatics.auckland.ac.nz/workshops/NGS-workshop-update.pdf
Mapping tutorial https://wikis.utexas.edu/display/bioiteam/Mapping+tutorial