<![CDATA[BOL: Next Generation Sequencing (NGS) Tutorials]]> https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials? https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials Sat, 24 Aug 2013 06:01:37 -0500 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials <![CDATA[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

==============================================

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/

]]> Jitendra Narayan https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-3703 Mon, 13 Jan 2020 11:30:43 -0600 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-3703 <![CDATA[Comment by LEGE]]> Informatics for RNA-seq: A web resource for analysis on the cloud https://github.com/griffithlab/rnaseq_tutorial?

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-2477 Tue, 21 Jun 2016 04:40:56 -0500 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-2477 <![CDATA[Comment by Shruti Paniwala]]> A field guide to whole-genome sequencing, assembly and annotation http://onlinelibrary.wiley.com/doi/10.1111/eva.12178/full

]]> Shruti Paniwala https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-2403 Fri, 13 May 2016 05:06:54 -0500 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-2403 <![CDATA[Comment by Radha Agarkar]]> This useful repository contains the files from the course in de novo assembly https://github.com/lexnederbragt/denovo-assembly-tutorial

]]> Radha Agarkar https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-2044 Fri, 19 Jun 2015 20:35:10 -0500 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-2044 <![CDATA[Comment by Rahul Nayak]]> A field guide to whole-genome sequencing, assembly and annotation http://onlinelibrary.wiley.com/doi/10.1111/eva.12178/full

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1885 Mon, 25 May 2015 16:36:02 -0500 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1885 <![CDATA[Comment by Jitendra Narayan]]> Sequencing depth and coverage: key considerations in genomic analyses

https://rtsf.natsci.msu.edu/_rtsf/assets/File/depth%20and%20coverage.pdf

]]> Jitendra Narayan https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1525 Sat, 12 Jul 2014 15:10:55 -0500 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1525 <![CDATA[Comment by Abhimanyu Singh]]> Challenges and Solutions in the Analysis of Next Generation Sequence Data http://lh3lh3.users.sourceforge.net/download/sam-20100630.pdf

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1524 Sat, 12 Jul 2014 15:05:15 -0500 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1524 <![CDATA[Comment by Neel]]> Mapping tutorial https://wikis.utexas.edu/display/bioiteam/Mapping+tutorial

]]> Neel https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1517 Sun, 06 Jul 2014 07:50:44 -0500 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1517 <![CDATA[Comment by Surabhi Chaudhary]]> NGS tutorial http://www.bioinformatics.auckland.ac.nz/workshops/NGS-workshop-update.pdf

]]> Surabhi Chaudhary https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1502 Mon, 23 Jun 2014 23:49:06 -0500 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1502 <![CDATA[Comment by John Parker]]> Next Generation Sequencing for DUMMIES http://users.ugent.be/~avierstr/nextgen/Next_generation_sequencing_web.pdf

]]> John Parker https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1460 Tue, 03 Jun 2014 10:46:16 -0500 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1460 <![CDATA[Comment by Rahul Nayak]]> NGS related research paper on Bioinformatics Journal @ http://www.oxfordjournals.org/our_journals/bioinformatics/nextgenerationsequencing.html

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1414 Wed, 21 May 2014 15:47:56 -0500 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1414 <![CDATA[Comment by Alok Prajapati]]> NGS tutorial for novice http://www.uni-mainz.de/FB/Biologie/Anthropologie/487_ENG_HTML.php

]]> Alok Prajapati https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1403 Mon, 12 May 2014 06:23:46 -0500 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1403 <![CDATA[Comment by Radha Agarkar]]> NGS tutorial at http://www.bioinformatics.auckland.ac.nz/workshops/NGS-workshop-update.pdf

]]> Radha Agarkar https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1369 Sat, 10 May 2014 01:27:18 -0500 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1369 <![CDATA[Comment by santosh pal]]> Bioinformatics algorithms at

www.users-birc.au.dk/cstorm/students/Vesterstroem_Mar2006.pdf

www.proteomics.bioengr.uic.edu/people/ezra/cv/thesis_uic.pdf

]]> santosh pal https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1294 Wed, 02 Apr 2014 11:10:07 -0500 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1294 <![CDATA[Comment by Jitendra Narayan]]> http://omictools.com/ an useful tools for omics data analysis ...

]]> Jitendra Narayan https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1273 Sat, 15 Mar 2014 17:20:11 -0500 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1273 <![CDATA[Comment by Jitendra Narayan]]> NGSUtils is a suite of software tools for working with next-generation sequencing datasets. Links http://ngsutils.org/

]]> Jitendra Narayan https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1271 Sat, 15 Mar 2014 17:07:26 -0500 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1271 <![CDATA[Comment by Jitendra Narayan]]> 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/

]]> Jitendra Narayan https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1142 Wed, 26 Feb 2014 16:41:38 -0600 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1142 <![CDATA[Comment by Surabhi Chaudhary]]> NGS tutorial http://lpm.hms.harvard.edu/palaver/sites/default/files/11_02_28_Dennis_Wall_1.pdf

]]> Surabhi Chaudhary https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1030 Tue, 03 Dec 2013 23:11:24 -0600 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1030 <![CDATA[Comment by Aaryan Lokwani]]>

Next-Generation Sequencing Workshop Materials

http://www.broadinstitute.org/science/programs/medical-and-population-genetics/next-generation-sequencing-workshop-materials

]]> Aaryan Lokwani https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1020 Thu, 28 Nov 2013 06:06:35 -0600 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-1020 <![CDATA[Comment by Kamalakshi Mukherjee]]> 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

]]> Kamalakshi Mukherjee https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-939 Thu, 14 Nov 2013 12:10:27 -0600 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-939 <![CDATA[Comment by Rahul Nayak]]> Next generation sequencing tutorial by illumina http://res.illumina.com/documents/products/illumina_sequencing_introduction.pdf

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-896 Fri, 08 Nov 2013 08:20:33 -0600 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-896 <![CDATA[Comment by Madhvan Reddy]]> GeneSifter: Next Generation Data Management and Analysis for Next Generation Sequencing http://www.geospiza.com/Products/WhitePaper_06102009.pdf

]]> Madhvan Reddy https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-895 Fri, 08 Nov 2013 08:02:22 -0600 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-895 <![CDATA[Comment by Madhvan Reddy]]> Link to recent developments and research papers on NGS algorithms https://www2.informatik.hu-berlin.de/~hakenber/links/nextgen.html

]]> Madhvan Reddy https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-548 Mon, 26 Aug 2013 07:10:02 -0500 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-548 <![CDATA[Comment by Jit]]> Samtools & Gbrowse2 for NGS tutorial http://gorgonzola.cshl.edu/pfb/2010/LectureNotes/ngs2/ngs2.pdf

]]> Jit https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-546 Sun, 25 Aug 2013 19:05:31 -0500 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-546 <![CDATA[Comment by Archana Malhotra]]> Challenges and Solutions in the Analysis of Next Generation Sequence Data

http://lh3lh3.users.sourceforge.net/download/sam-20100630.pdf

]]> Archana Malhotra https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-545 Sun, 25 Aug 2013 18:57:02 -0500 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#item-annotation-545 <![CDATA[Comment by Archana Malhotra]]> 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

]]> Archana Malhotra