Choice of next-generation sequencing pipelines

Area of Science:

• Genetics and Genomics
• Bioinformatics
• Molecular Biology

Background:

• Next-generation sequencing (NGS) technologies have significantly advanced genetic research in the 21st century.
• NGS is poised to replace existing high-throughput technologies due to its ability to generate vast amounts of sequence data.
• NGS applications are crucial for decoding biological systems, including genome anatomy, gene mapping, and transcriptome analysis.

Purpose of the Study:

• To discuss the management of successful next-generation sequencing (NGS) pipelines.
• To cover project planning, platform selection, and data analysis management for NGS.
• To highlight the impact of NGS on genetic decoding and genome-wide studies.

Main Methods:

• De-novo genomic sequencing (mate-paired and whole-genome shotgun strategies).
• Targeted gene sequencing for large bacterial communities.
• RNA-sequencing (RNA-seq) methods, including whole transcriptome sequencing and Serial Analysis of Gene Expression (Sage-analysis).

Main Results:

• NGS protocols overcome technical issues like mapping specificity and enable detection of structural variations.
• Advanced NGS methods improve gene annotation and bridge sequencing gaps.
• NGS pipelines are fundamental for genome-wide fields such as metagenomics.

Conclusions:

• NGS technologies are indispensable tools for modern genetic and genomic research.
• Effective management of NGS pipelines, from planning to data analysis, is critical for successful outcomes.
• NGS continues to drive significant advances in understanding biological systems at a genomic level.