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Related Experiment Video

Updated: Jun 16, 2026

Cost-Efficient Transcriptomic-Based Drug Screening

Cost-Efficient Transcriptomic-Based Drug Screening

Published on: February 23, 2024

SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read.

Juan Falgueras¹, Antonio J Lara, Noé Fernández-Pozo

¹Departamento de Lenguajes y Ciencias de la Computación, Universidad de Málaga, Málaga, Spain.

BMC Bioinformatics

|January 22, 2010

Summary

SeqTrim is an efficient pipeline for pre-processing DNA sequences, including next-generation sequencing data. It removes artefacts and improves sequence quality, outperforming other pre-processing tools.

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Last Updated: Jun 16, 2026

Cost-Efficient Transcriptomic-Based Drug Screening

Cost-Efficient Transcriptomic-Based Drug Screening

Published on: February 23, 2024

Area of Science:

Bioinformatics
Genomics
Computational Biology

Background:

High-throughput sequencing generates vast amounts of data, necessitating high-quality and reliable sequences.
Database contamination from artefactual sequences is a growing concern, exacerbated by technologies like pyrosequencing.
Customizable pre-processing algorithms are essential for managing and ensuring the accuracy of sequencing data.

Purpose of the Study:

To develop and implement SeqTrim, an efficient pipeline for pre-processing diverse sequence reads.
To provide a configurable tool that identifies and removes various sequence artefacts.
To enhance sequence quality and reliability for downstream genomic analyses.

Main Methods:

SeqTrim integrates existing and novel algorithms for sequence pre-processing.
It identifies and removes low-quality, vector, adaptor, low complexity, and contaminant sequences.
The pipeline detects chimeric reads and sequence inserts, offering multiple input/output formats for workflow integration.

Main Results:

SeqTrim is available as a web and standalone command-line application.
It effectively removes artefacts without over-trimming, performing well across various library types (EST, SSH, genomic DNA) and pyrosequencing reads.
SeqTrim demonstrates superior performance compared to other pre-processing tools.

Conclusions:

SeqTrim is an efficient and configurable pipeline for pre-processing all types of sequence reads, including next-generation sequencing.
Its user-friendly interface allows detailed monitoring of pre-processing stages and individual sequence verification.
SeqTrim provides more comprehensive information and better artefact removal than existing pre-processors.