NGSPanPipe: A Pipeline for Pan-genome Identification in Microbial Strains from Experimental Reads
| Autor: | Punit Kaur, Umay Kulsum, Arti Kapil, Harpreet Singh |
|---|---|
| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Computer science 030106 microbiology Sequence assembly Pan-genome Bacterial genome size Computational biology Genome Pipeline (software) DNA sequencing 03 medical and health sciences ComputingMethodologies_PATTERNRECOGNITION 030104 developmental biology Identification (biology) Perl computer computer.programming_language |
| Zdroj: | Advances in Experimental Medicine and Biology ISBN: 9789811075711 |
| DOI: | 10.1007/978-981-10-7572-8_4 |
| Popis: | Recent advancements in sequencing technologies have decreased both time span and cost for sequencing the whole bacterial genome. High-throughput Next-Generation Sequencing (NGS) technology has led to the generation of enormous data concerning microbial populations publically available across various repositories. As a consequence, it has become possible to study and compare the genomes of different bacterial strains within a species or genus in terms of evolution, ecology and diversity. Studying the pan-genome provides insights into deciphering microevolution, global composition and diversity in virulence and pathogenesis of a species. It can also assist in identifying drug targets and proposing vaccine candidates. The effective analysis of these large genome datasets necessitates the development of robust tools. Current methods to develop pan-genome do not support direct input of raw reads from the sequencer machine but require preprocessing of reads as an assembled protein/gene sequence file or the binary matrix of orthologous genes/proteins. We have designed an easy-to-use integrated pipeline, NGSPanPipe, which can directly identify the pan-genome from short reads. The output from the pipeline is compatible with other pan-genome analysis tools. We evaluated our pipeline with other methods for developing pan-genome, i.e. reference-based assembly and de novo assembly using simulated reads of Mycobacterium tuberculosis. The single script pipeline (pipeline.pl) is applicable for all bacterial strains. It integrates multiple in-house Perl scripts and is freely accessible from https://github.com/Biomedinformatics/NGSPanPipe. |
| Databáze: | OpenAIRE |
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