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/

More at http://busco.ezlab.org/

Address of the bookmark: http://busco.ezlab.org/

TULIP currently consists of to Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as prototypes, and additional components and/or implementations are likely to follow. 
Tulipseed takes as input alignments files of long reads to sparse short seeds, and outputs a graph and scaffold structures. Tulipbulb adds long read sequencing data to these.

https://github.com/Generade-nl/TULIP

Address of the bookmark: https://github.com/Generade-nl/TULIP

Address of the bookmark: https://sanger-pathogens.github.io/Roary/

Bactopia can be split into two main parts: Bactopia Analysis Pipeline, and Bactopia Tools.

Bactopia Analysis Pipeline is the main per-isolate workflow in Bactopia. Built with Nextflow, input FASTQs (local or available from SRA/ENA) are put through numerous analyses including: quality control, assembly, annotation, minmer sketch queries, sequence typing, and more.

Bactopia Tools are a set a independent workflows fo

Address of the bookmark: https://github.com/bactopia/bactopia

National Bioinformatics Infrastructure Sweden (NBIS) (nbis.se) plays an important role in advancing life science research in Sweden by providing expert support and developing cutting-edge bioinformatics infrastructure. Operating as a truly national initiative, NBIS employs more than 120 bioinformaticians, system developers, and data stewards across multiple locations in Sweden. It serves as the bioinformatics platform at SciLifeLab, a national resource that facilitates research in molecular biosciences by offering access to state-of-the-art technologies and technical expertise. With strong ties to data-producing facilities and ongoing collaborations with leading research groups, NBIS is ideally positioned to support world-class bioinformatics analyses. Furthermore, NBIS is the Swedish node in ELIXIR, the European infrastructure for biological information.

NBIS is seeking an experienced bioinformatician to support both Swedish and international projects. As part of our dynamic team, you will work closely with researchers to process large-scale biological data and contribute to advancing our data analysis infrastructure. Strong problem-solving skills, attention to detail, and the ability to troubleshoot complex bioinformatics pipelines are essential for success in this role. Flexibility and a willingness to learn are also important, as NBIS continually adapts to meet the evolving needs of the Swedish research community.

More at https://www.uu.se/en/about-uu/join-us/jobs-and-vacancies/job-details?query=778701

The software is implemented in Python 3 and runs in both Python 2.7 and 3.4– on Macintosh and Linux systems. It is freely available at https://github.com/nigyta/dfast_core/ under the GPLv3 license with external binaries bundled in the software distribution. An on-line version is also available at https://dfast.nig.ac.jp/.

Address of the bookmark: https://dfast.nig.ac.jp/

Unless otherwise noted, all terminology below is consistent with this paper, and all references to figures and tables in this readme refer to this paper. Specifically, some of the terminology used below is outlined in Figure S2. The assembly procedure is described in detail in the Supporting Online Materials, specifically in the section labelled “Pipeline description”.

In addition, the pipeline uses tools and methods from Juicer (Durand & Shamim et al., Cell Systems, 2016) and Juicebox (Durand & Robinson et al., Cell Systems, 2016), as well as additional dependencies noted below.

Feel free to post your questions and comments at: http://www.aidenlab.org/forum.html

http://aidenlab.org/documentation.html

Address of the bookmark: https://github.com/theaidenlab/3d-dna

Documentation can be found at https://nanoporetech.github.io/katuali/.

Address of the bookmark: https://github.com/nanoporetech/katuali

HaploTypo is implemented in Python 2.7 and Python 3.5, and is freely available at https://github.com/gabaldonlab/haplotypo, and as a Docker image.

Address of the bookmark: https://github.com/gabaldonlab/haplotypo