FastqPuri: high-performance preprocessing of RNA-seq data

BMC Bioinformatics

Table 1 Provided functionality of FastqPuri and existing tools

Tool name	language	input	QC	QF	Ad	cont	PE	Year
FastqPuri	C, R	fq*	√	√	√	√	√	2019
fastp [6]	C++	fq,gz	√	√	√	×	√	2018
Fastq Screen [18]	perl	fq	×	×	×	√	×	2018
RNA-QC-Chain [20]	C++	fq,fa	∼	√	√	∼	√	2018
afterQC [5]	C,python	fq	√	∼	√	×	√	2017
Cutadapt [13]	C,python	fq,fa,gz	×	∼	√	×	√ ^{Footnote 1}	2011
trimmomatic [3]	java	fq,gz	×	√	√	×	√	2014
Biobloom [7]	C++	BAM/SAM,fa,fq*	×	×	×	√	√	2014
FastQC [1]	java	fq,gz	√	×	×	×	×	2010
SolexaQA++ [8]	C++,R	fq,gz	√	√	×	×	×	2010
RSeQC [17]	C,python	BAM/SAM	√	×	×	×	×	2012
RNA-SeQC [9]	java	BAM	√	×	×	∼	×	2012
QoRTs [11]	java,R	BAM	√	×	×	×	×	2015

lang: programming language, QC: quality control, QF: low quality filtering, Ad: removes technical sequences such as adapters, cont: removes contaminations, PE: handles paired end data, Year: year of publication. fq* stands for uncompressed fastq or fastq compressed in gz, bz2, xz and for FastqPuri also Z format. For both FastqPuri and Biobloom, input may be tarred. [1] functionality was added later

ISSN: 1471-2105