FastqPuri: high-performance preprocessing of RNA-seq data

URN to cite this document: urn:nbn:de:bvb:355-epub-400963

Peréz-Rubio, Paula, Lottaz, Claudio and Engelmann, Julia C. (2018) FastqPuri: high-performance preprocessing of RNA-seq data. bioRxiv. (Submitted)

Preview

License: Creative Commons Attribution 4.0
PDF
Download (1MB)

Date of publication of this fulltext: 26 Apr 2019 07:08

at publisher (via DOI)

Other URL: https://www.biorxiv.org/content/10.1101/480707v1.full

Abstract

Abstract

Background 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.

Results We here 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. We benchmarked FastqPuri against existing tools and found that FastqPuri is superior in terms of speed, memory usage, versatility and comprehensiveness. Conclusions: 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. FastqPuri is available at https://github.com/jengelmann/FastqPuri. It is implemented in C and R and licensed under GPL v3.

Export bibliographical data

Item type:

Article

Date:

December 2018

Institutions:

Medicine > Institut für Funktionelle Genomik > Lehrstuhl für Statistische Bioinformatik (Prof. Spang)

Identification Number:

Value	Type
10.1101/480707	DOI

Dewey Decimal Classification:

600 Technology > 610 Medical sciences Medicine

Status:

Submitted

Refereed:

No, this version has not been refereed yet (as with preprints)

Created at the University of Regensburg:

Yes

Item ID:

40096

Owner only: item control page

Download Statistics

Downloads

Downloads per month over past year

Altmetric

CORE (COnnecting REpositories)

Abstract

Abstract

Export bibliographical data

Downloads

University Library