**8.1. Genomics**

**Program Website**

*7. Optical mappers*

**"omics"**

Personal Genome Project http://www.personalgenomes.org 1000 Genomes Project http://www.1000genomes.org HapMap http://hapmap.ncbi.nlm.nih.gov/

UCSC browser https://genome.ucsc.edu Ensembl browser http://www.ensembl.org Jbrowse browser http://jbrowse.org

24 Next Generation Sequencing - Advances, Applications and Challenges

Web Apollo browser http://genomearchitect.org

KEGG http://www.genome.jp/kegg/

*8. NGS and bioinformatics software providers and biological databases* Omicsmap for NGS http://omicsmaps.com/

Genomeweb https://www.genomeweb.com

Bioinformatic software http://seqanswers.com/wiki/Software/list

Applied Bioinformatics http://www.appliedbioinformatics.com.au

**Table 3.** Useful websites for NGS tools, browsers, portals, providers, and online databases.

Bioinformatics Web http://www.bioinformaticsweb.net

The Sequencing Marketplace http://allseq.com

BioNano mapper http://www.bionanogenomics.com

NCBI mapview http://www.ncbi.nlm.nih.gov/projects/mapview/ NCBI resources http://www.ncbi.nlm.nih.gov/guide/all/ - tab-all\_

Whole-Genome Mapping http://opgen.com/genomic-services/what-is-whole-genome-mapping

The NGS WikiBook http://en.wikibooks.org/wiki/Next\_Generation\_Sequencing\_(NGS)

Biological databases https://en.wikipedia.org/wiki/List\_of\_biological\_databases

http://bioinformaticssoftwareandtools.co.in

**8. Impact and applications of NGS: Opening the doors into the world of**

All hereditary information is contained within the structure, organization, and function of an organism's genome. The continual emergence of many new public bioinformatics databases (Table 3) on the World Wide Web demonstrates and reflects the impact of NGS on the life sciences and our need to constantly develop new methods to interrogate and decode hereditary

https://en.wikipedia.org/wiki/List\_of\_open-source\_bioinformatics\_software

A detailed organizational analysis and an understanding of the full landscape of a genome are possible only after *de novo* whole-genome shotgun sequencing and annotation has been performed [11]. WGS has had an enormous impact on viral, bacterial, and archaeal genomics [114–117]. Some of these successes are provided in the metagenomics section (see section *8.5*). Others have reviewed the impact of WGS and genomics on fungi [118, 119], algae [120], animals [121, 122], and humans [10, 13, 123–127]. WGS has become increasingly easier, faster, and cheaper because of technological improvements and the availability of hundreds of sequenced genomes that can be used as references for annotation. Although it seems unlikely that the genomes of all the 11 million extant worldwide species will ever be or need to be sequenced, the genomic sequences for a large number of eukaryote species are already available for scientific scrutiny, including the genomes of some endangered vertebrate species that may need assistance in the management of their breeding and survival [122]. In 2009, an interna‐ tional consortium established the Genome 10K Project to sequence and analyze the complete genomes of 10,000 vertebrate species (http://genome10k.org).

NGS has blasted human genomics into an exciting new era of genetic investigation geared towards humanomics and disease (see section *8.9*) and the management of an individual's life cycle and health issues by way of personal genomes or personomics [123]. Targeted or wholegenome resequencing of individuals from within the same or different species is aimed to detect and catalogue SNPs, mutations, and sequence variants such as indels, copy number, and structural variations [14–16]. PCR-based candidate gene and whole-exome analysis are two widely used methods that can be performed with higher coverage and at much lower cost than whole-genome resequencing. Genotyping HLA genes of humans for clinical diagnosis or research by sequencing the entire gene [97, 128] or just the exons [129] is an example of targeted resequencing to identify polymorphisms that are important in tissue or cell matching for transplantation [130]. Exomics is targeted specifically towards coding genes and discovering exonic mutations responsible for rare Mendelian disorders such as hearing loss, intellectual disabilities, and movement disorders and for investigating common disorders such as heart disease, hypertension, diabetes, and cancer [13, 123, 125], and many others that are listed at the Online Mendelian Inheritance in Man (OMIM) database (Table 3, [49]). In contrast to WES, WGS can assess alterations in the coding genes and the regulatory and noncoding regions [123, 126], especially multiallelic copy number variations [127]. Cancer research has shown that it is important to target all types of somatic/germ-line genetic alterations, including nucleotide substitutions, small insertions and deletions (indels), CNVs, and chromosomal rearrange‐ ments in the noncoding regions [13, 15, 123]. WGS has been used to identify variants, indels, and multiple numbers of genes involved in rare and common diseases such as Charcot-Marie-Tooth neuropathy, dopa-responsive dystonia, acquired essential thrombocytosis, erythrocy‐ tosis, and many others [123, 126].
