SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files

Sequence files formats (FASTA and FASTQ) are commonly used in bioinformatics, molecular biology and biochemistry. With the advent of next-generation sequencing (NGS) technologies, the number of FASTQ datasets produced and analyzed has grown exponentially, urging the development of dedicated software to handle, parse, and manipulate such files efficiently. Several bioinformatics packages are available to filter and manipulate FASTA and FASTQ files, yet some essential tasks remain poorly supported, leaving gaps that any workflow analysis of NGS datasets must fill with custom scripts. This can introduce harmful variability and performance bottlenecks in pivotal steps. Here we present a suite of tools, called SeqFu (Sequence Fastx utilities), that provides a broad range of commands to perform both common and specialist operations with ease and is designed to be easily implemented in high-performance analytical pipelines. SeqFu includes high-performance implementation of algorithms to interleave and deinterleave FASTQ files, merge Illumina lanes, and perform various quality controls (identification of degenerate primers, analysis of length statistics, extraction of portions of the datasets). SeqFu dereplicates sequences from multiple files keeping track of their provenance. SeqFu is developed in Nim for high-performance processing, is freely available, and can be installed with the popular package manager Miniconda.