FastaValidator: an open-source Java library to parse and validate FASTA formatted sequences

BMC Research Notes

Frank Oliver Glöckner²  Timmy Schweer³  Wolfgang Hankeln¹  Jan Gerken²  Jost Waldmann² 

[1] Mediomix GmbH, Eupener Straße 139, 50933 Köln, Germany;Jacobs University Bremen gGmbH, Campusring 1, 28759 Bremen, Germany;Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany

关键词: High-throughput;    Data validation;    FASTA;   

Others  :  1132479
DOI  :  10.1186/1756-0500-7-365

 received in 2014-01-22, accepted in 2014-06-10,  发布年份 2014

【 摘 要 】

Background

Advances in sequencing technologies challenge the efficient importing and validation of FASTA formatted sequence data which is still a prerequisite for most bioinformatic tools and pipelines. Comparative analysis of commonly used Bio*-frameworks (BioPerl, BioJava and Biopython) shows that their scalability and accuracy is hampered.

Findings

FastaValidator represents a platform-independent, standardized, light-weight software library written in the Java programming language. It targets computer scientists and bioinformaticians writing software which needs to parse quickly and accurately large amounts of sequence data. For end-users FastaValidator includes an interactive out-of-the-box validation of FASTA formatted files, as well as a non-interactive mode designed for high-throughput validation in software pipelines.

Conclusions

The accuracy and performance of the FastaValidator library qualifies it for large data sets such as those commonly produced by massive parallel (NGS) technologies. It offers scientists a fast, accurate and standardized method for parsing and validating FASTA formatted sequence data.

【 授权许可】

   
2014 Waldmann et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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