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Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

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RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
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Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Updated: Aug 5, 2025

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

A machine-readable specification for genomics assays.

A Sina Booeshaghi¹, Xi Chen², Lior Pachter^1,3

¹Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California.

Biorxiv : the Preprint Server for Biology

|March 30, 2023

Summary

This summary is machine-generated.

This study introduces seqspec, a machine-readable specification for genomics libraries. It standardizes preprocessing, enabling better tracking and comparison of genomics assays across different technologies.

Area of Science:

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Genomics

Bioinformatics

Computational Biology

Background:

Genomics library preprocessing requires custom scripts due to diverse assays and sequencing technologies.
Lack of standardization hinders efficient data processing and comparison across studies.

Conclusions:

seqspec promotes standardization in genomics data preprocessing.
The specification and tool aid in managing and comparing diverse genomics assays effectively.