QuAdTrim: Overcoming computational bottlenecks in sequence quality control

Abstract

With the recent torrent of high throughput sequencing (HTS) data the necessity for highly efficient algorithms for common tasks is paramount. One task for which the basis for all further analysis of HTS data is initial data quality control, that is, the removal or trimming of poor quality reads from the dataset. Here we present QuAdTrim, a quality control and adapter trimming algorithm for HTS data that is up to 57 times faster and uses less than 0.06% of the memory of other commonly used HTS quality control programs. QuAdTrim will reduce the time and memory required for quality control of HTS data, and in doing, will reduce the computational demands of a fundamental step in HTS data analysis. Additionally, QuAdTrim impliments the removal of homopolymer Gs from the 3' end of sequence reads, a common error generated on the NovaSeq, NextSeq and iSeq100 platforms. Availability and ImplementationThe source code is freely available on bitbucket under a BSD licence, see COPYING file for details: https://bitbucket.org/arobinson/quadtrim Contact Andrew Robinson andrewjrobinson at gmail dot com

Using expression data to fine map QTL associated with fertility in dairy cattle

“…Sequencing libraries were prepared using the NEXTFLEX Rapid Directional RNA-Seq Library Prep Kit (PerkinElmer) according to the manufacturer’s instructions and run on a NovaSeq6000 genome analyser (Illumina Inc) in a 150 cycle paired-end run. The read quality of FastQ files was assessed using the FastQC program [ 28 ], and FastQ files were trimmed and filtered using the QuadTrim algorithm with a minimum read length of 50, a maximum of five poor-quality bases and a minimum base cut-off quality of 20 [ 29 ]. Subsequently, STAR 2-pass mapping [ 30 ] was performed for alignment of the RNA reads to the ARS-UCD1.2 reference assembly that is merged with the Btau5 Y chromosome and the Ensembl annotation release 97.…”

The genome of tropically adapted Brahman cattle (Bos taurus indicus) reveals novel genome variation in production animals

“…Illumina sequences were trimmed with QUADtrim [27] including removal of adapter sequences by read overlap, removal or low quality bases from both the start and end of the reads, and removal of trailing G’s, which is an artefact of the color chemistry on the current iteration of the Novaseq.…”

Integrating genome-wide association and expression quantitative trait loci (eQTL) analyses identifies genes affecting fertility in cattle and suggests a common set of genes regulating fertility in mammals

“…Briefly, QuadTrim 49 was used to trim and filter poor-quality bases and sequence reads. Adaptor sequences were trimmed based on pair overlap and bases with a quality score of < 20 were removed.…”