Rapid evaluation and quality control of next generation sequencing data with FaQCs

BMC Bioinformatics

Chien-Chi Lo¹  Patrick S G Chain² 

[1] Bioenergy and Biome Sciences Group, Los Alamos National Laboratory, Los Alamos 87545, NM, USA

[2] Genome Science Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos 87545, NM, USA

关键词: Data preprocessing;    Next generation sequencing analysis;    Trimming;    Quality control;   

Others  :  1085074
DOI  :  10.1186/s12859-014-0366-2

 received in 2014-07-03, accepted in 2014-10-29,  发布年份 2014

【 摘 要 】

Background

Next generation sequencing (NGS) technologies that parallelize the sequencing process and produce thousands to millions, or even hundreds of millions of sequences in a single sequencing run, have revolutionized genomic and genetic research. Because of the vagaries of any platform’s sequencing chemistry, the experimental processing, machine failure, and so on, the quality of sequencing reads is never perfect, and often declines as the read is extended. These errors invariably affect downstream analysis/application and should therefore be identified early on to mitigate any unforeseen effects.

Results

Here we present a novel FastQ Quality Control Software (FaQCs) that can rapidly process large volumes of data, and which improves upon previous solutions to monitor the quality and remove poor quality data from sequencing runs. Both the speed of processing and the memory footprint of storing all required information have been optimized via algorithmic and parallel processing solutions. The trimmed output compared side-by-side with the original data is part of the automated PDF output. We show how this tool can help data analysis by providing a few examples, including an increased percentage of reads recruited to references, improved single nucleotide polymorphism identification as well as de novo sequence assembly metrics.

Conclusion

FaQCs combines several features of currently available applications into a single, user-friendly process, and includes additional unique capabilities such as filtering the PhiX control sequences, conversion of FASTQ formats, and multi-threading. The original data and trimmed summaries are reported within a variety of graphics and reports, providing a simple way to do data quality control and assurance.

【 授权许可】

   
2014 Lo and Chain; licensee BioMed Central Ltd.

【 图 表 】

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