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Next-generation Sequencing

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.

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Related Experiment Video

Updated: May 18, 2026

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

Published on: May 19, 2019

ESTclean: a cleaning tool for next-gen transcriptome shotgun sequencing.

Hongseok Tae¹, Dongsung Ryu, Suhas Sureshchandra

¹The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47401, USA.

BMC Bioinformatics

|September 27, 2012

Summary

This summary is machine-generated.

ESTclean is a new software package designed to clean raw cDNA sequences from next-generation sequencing (NGS) protocols. It improves transcriptome study accuracy by removing contaminants like adapters and primers, enhancing sequence quality control.

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Area of Science:

Bioinformatics
Genomics
Molecular Biology

Background:

Next-generation sequencing (NGS) technologies, particularly full cDNA shotgun sequencing, are crucial for transcriptome studies.
Various 454 sequencing protocols utilize distinct DNA tags/adapters, potentially introducing contaminants.
Contaminants can lead to mis-assembly and inaccurate sequencing products, impacting data reliability.

Purpose of the Study:

To develop a robust software solution for cleaning raw cDNA sequencing data.
To address the challenges posed by contaminants in diverse NGS protocols.
To enhance the accuracy and reliability of transcriptome sequencing.

Main Methods:

Implementation of a new program with a graphical user interface and batch script functionality.
Development of a multi-module cleaning process including barcode, adapter, primer, and poly-A tail trimming.
Inclusion of vector screening and low-quality region trimming modules for comprehensive data cleaning.

Main Results:

A novel software package, ESTclean, has been successfully designed and implemented.
The software effectively performs raw sequence cleaning through a combination of specialized modules.
ESTclean demonstrates superior performance in cleaning sequences from complex protocols using barcodes and multiple primers.

Conclusions:

ESTclean is a versatile software package for cleaning cDNA sequences and aiding in sequencing protocol development.
It provides valuable summary tables and figures for quality control via a graphical user interface.
The software is particularly effective for complex sequencing protocols, improving overall data quality and analysis.