Abstract
Next generation sequencing (NGS) innovations put a compelling landmark in life science and changed the direction of research in clinical oncology with its productivity to diagnose and treat cancer. The aim of our portal comprehensive resources for cancer NGS data analysis (CRCDA) is to provide a collection of different NGS tools and pipelines under diverse classes with cancer pathways and databases and furthermore, literature information from PubMed. The literature data was constrained to 18 most common cancer types such as breast cancer, colon cancer and other cancers that exhibit in worldwide population. NGS-cancer tools for the convenience have been categorized into cancer genomics, cancer transcriptomics, cancer epigenomics, quality control and visualization. Pipelines for variant detection, quality control and data analysis were listed to provide out-of-the box solution for NGS data analysis, which may help researchers to overcome challenges in selecting and configuring individual tools for analysing exome, whole genome and transcriptome data. An extensive search page was developed that can be queried by using (i) type of data [literature, gene data and sequence read archive (SRA) data] and (ii) type of cancer (selected based on global incidence and accessibility of data). For each category of analysis, variety of tools are available and the biggest challenge is in searching and using the right tool for the right application. The objective of the work is collecting tools in each category available at various places and arranging the tools and other data in a simple and user-friendly manner for biologists and oncologists to find information easier. To the best of our knowledge, we have collected and presented a comprehensive package of most of the resources available in cancer for NGS data analysis. Given these factors, we believe that this website will be an useful resource to the NGS research community working on cancer.Database URL: http://bioinfo.au-kbc.org.in/ngs/ngshome.html.
Highlights
The chain termination method by Sanger and sequencing method by Maxam-Gilbert overturned the biomedical world through an efficient sequencing approach at significantly lower costs [1, 2]
Procedures in next generation sequencing (NGS) include extracting DNA/RNA from samples, making a library of sections that are sequenced in parallel to short reads, and are reassembled by aligning them to a reference genome
Cancer genomics denote sequencing a genome that is confined to a particular tumor tissue and mapping the short reads obtained to a reference genome
Summary
The chain termination method by Sanger and sequencing method by Maxam-Gilbert overturned the biomedical world through an efficient sequencing approach at significantly lower costs [1, 2]. The main difference between Sanger sequencing data and generation sequencing (NGS) data is the read length or the quantity of nucleotides acquired. NGS is a recent innovation that empowers massively parallel sequencing reactions along these lines diminishing the specimen size and reagent costs. Procedures in NGS include extracting DNA/RNA from samples, making a library of sections that are sequenced in parallel to short reads, and are reassembled by aligning them to a reference genome. In this way, the entire genome is obtained from the arrangement of consensus reads. The reads obtained from these platforms can be aligned and further analysed by using various NGS tools
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