FastqPuri – high-performance preprocessing of RNA-Seq data

RNA sequencing (RNA-seq) has become the standard means of analyzing gene and transcript expression in high-throughput. While previously sequence alignment was a time demanding step, fast alignment methods and even more so transcript counting methods which avoid mapping and quantify gene and transcript expression by evaluating whether a read is compatible with a transcript, have led to significant speed-ups in data analysis. Now, the most time demanding step in the analysis of RNA-seq data is preprocessing the raw sequence data, such as running quality control and adapter, contamination and quality filtering before transcript or gene quantification. To do so, many researchers chain different tools, but a comprehensive, flexible and fast software that covers all preprocessing steps is currently missing.

University of Regensburg researchers present FastqPuri, a light-weight and highly efficient preprocessing tool for fastq data. FastqPuri provides sequence quality reports on the sample and dataset level with new plots which facilitate decision making for subsequent quality filtering. Moreover, FastqPuri efficiently removes adapter sequences and sequences from biological contamination from the data. It accepts both single- and paired-end data in uncompressed or compressed fastq files. FastqPuri can be run stand-alone and is suitable to be run within pipelines. The researchers benchmarked FastqPuri against existing tools and found that FastqPuri is superior in terms of speed, memory usage, versatility and comprehensiveness.

Workflow for preprocessing fastq files with FastqPuri


Qreport generates a quality report in html format for each sample, while Sreport generates one summary quality report for all samples. Depending on the size of the sequence file with potential contaminations, makeTree or makeBloom generates a data structure for filtering contaminations. trimFilter (or trimFilterPE for paired-end data) filters and trims reads containing adapters or adapter remnants, biological contaminations and low quality bases. On the filtered reads, Qreport and Sreport can be run again to ensure that the filtered data meets the user’s expectations. Legend: yellow: fastq files, red: FastqPuri executables, green: FastqPuri quality reports in html format

FastqPuri is a new tool which covers all aspects of short read sequence data preprocessing. It was designed for RNA-seq data to meet the needs for fast preprocessing of fastq data to allow transcript and gene counting, but it is suitable to process any short read sequencing data of which high sequence quality is needed, such as for genome assembly or SNV (single nucleotide variant) detection. FastqPuri is most flexible in filtering undesired biological sequences by offering two approaches to optimize speed and memory usage dependent on the total size of the potential contaminating sequences.

Availability – FastqPuri is available at . It is implemented in C and R and licensed under GPL v3.

Pérez-Rubio P1, Lottaz C1, Engelmann JC2. (2019) FastqPuri: high-performance preprocessing of RNA-seq data. BMC Bioinformatics 20(1):226. [article]

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