FastQFS – A tool for evaluating and filtering paired-end sequencing data generated from high throughput sequencing

Abstract

Next generation sequencing (NGS) technologies generate huge amounts of sequencing data. Several microbial genome projects, in particular for fungal whole genome sequencing, have used NGS techniques because of their cost efficiency. However, NGS techniques also require computational tools able to process and analyze huge datasets. Data processing steps, including quality and length filters, often lead to a remarkable improvement in the accuracy and quality of data analyses. Choosing appropriate parameters for this purpose is not always straightforward, as these will vary with the dataset. In this study we present the FastQFS (Fastq Quality Filtering and Statistics) tool, which can be used for both an assessment of filtering parameters and read filtering. There are several tools available, but an important asset of FastQFS is that it provides the information of filtering parameters that fit best to the raw dataset, prior to computationally expensive filtering. It generates statistics of reads meeting different quality and length thresholds, and also the expected coverage depth of the genome which would be achieved after applying different filtering parameters. Thus, the FastQFS tool will help researchers to make informed decisions on an NGS read filtering parameters, and avoiding timeconsuming optimization of filtering criteria after initial analyses. The source code of the tool and related files are available from 10.12761/SGN.2015.4.

Adaptive differentiation coincides with local bioclimatic conditions along an elevational cline in populations of a lichen-forming fungus

“…We filtered out reads shorter than 80 bp, reads with N's, and reads with average base quality scores less than 26 along with their pairs using FastQFS [ 40 ]. Trimmed paired-end reads of each pool were mapped to the L. pustulata genome using BWA-MEM [ 41 ] and default parameters.…”

The genome ofPeronospora belbahriireveals high heterozygosity, a low number of canonical effectors and CT-rich promoters

“…Reads shorter than 65 bp were filtered out. The second round of filtering was performed using FastQFS (Sharma and Thines 2015). Read pairs were eliminated if either read had an ambiguous base, or if an individual base had a Phred-scale quality score of 3 or lower, or if the average Phred score was below 26.…”

Comparative Genomics Including the Early-Diverging Smut FungusCeraceosorus bombacisReveals Signatures of Parallel Evolution within Plant and Animal Pathogens of Fungi and Oomycetes

“…Sequencing was carried out by a commercial sequencing provider (LGC Genomics). Illumina adapter-clipped and primer-clipped gDNA reads of 300, 600 bp, 3, and 8 kb insert libraries were further processed by quality and length filters using FastQFS ( Sharma and Thines 2015 ). Reads having an average quality below 26 phred score, a length shorter than 72 bp, and having ambiguous bases were discarded from the analyses.…”