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HTQC: a fast quality control toolkit for Illumina sequencing data

Xi Yang1, Di Liu1, Fei Liu1, Jun Wu1, Jing Zou1, Xue Xiao1, Fangqing Zhao2 and Baoli Zhu1*

Author affiliations

1 CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, NO.1 West Beichen Road, Chaoyang District, Beijing, China

2 Beijing Institutes of Life Sciences, Chinese Academy of Sciences, NO.1 West Beichen Road, Chaoyang District, Beijing, China

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Citation and License

BMC Bioinformatics 2013, 14:33  doi:10.1186/1471-2105-14-33

Published: 31 January 2013

Abstract

Background

Illumina sequencing platform is widely used in genome research. Sequence reads quality assessment and control are needed for downstream analysis. However, software that provides efficient quality assessment and versatile filtration methods is still lacking.

Results

We have developed a toolkit named HTQC – abbreviation of High-Throughput Quality Control – for sequence reads quality control, which consists of six programs for reads quality assessment, reads filtration and generation of graphic reports.

Conclusions

The HTQC toolkit can generate reads quality assessment faster than existing tools, providing guidance for reads filtration utilities that allow users to choose different strategies to remove low quality reads.