XS: a FASTQ read simulator

Abstract

BackgroundThe emerging next-generation sequencing (NGS) is bringing, besides the natural huge amounts of data, an avalanche of new specialized tools (for analysis, compression, alignment, among others) and large public and private network infrastructures. Therefore, a direct necessity of specific simulation tools for testing and benchmarking is rising, such as a flexible and portable FASTQ read simulator, without the need of a reference sequence, yet correctly prepared for producing approximately the same characteristics as real data.FindingsWe present XS, a skilled FASTQ read simulation tool, flexible, portable (does not need a reference sequence) and tunable in terms of sequence complexity. It has several running modes, depending on the time and memory available, and is aimed at testing computing infrastructures, namely cloud computing of large-scale projects, and testing FASTQ compression algorithms. Moreover, XS offers the possibility of simulating the three main FASTQ components individually (headers, DNA sequences and quality-scores).ConclusionsXS provides an efficient and convenient method for fast simulation of FASTQ files, such as those from Ion Torrent (currently uncovered by other simulators), Roche-454, Illumina and ABI-SOLiD sequencing machines. This tool is publicly available at http://bioinformatics.ua.pt/software/xs/.

An alignment-free method to find and visualise rearrangements between pairs of DNA sequences

“…Therefore, at a first stage, we end up with a numerical information sequence of size . Fig 1 illustrates how the method operates, using synthetic data generated with an appropriate tool 48 . The target was created by manipulating some parts of the reference, as described in the figure.…”

Learning the Comparing and Converting Method of Sequence Phred Quality Score

“…FASTQ read simulation has been approached by several tools [7] [8]. A comparison of those tools can be seen in [9].…”

Fast functional annotation of metagenomic shotgun data by DNA alignment to a microbial gene catalog

“…Additional data sets were downloaded from MG--RAST [9] for mouse gut (MG--RAST 4535626.3) and for copper mine waste (MG--RAST 4664533.3). Simulated FASTQ data files were created from the human GRCh38 reference genome and the E. coli K12 reference genome (GenBank: accession U00096.3) by MetaSim [10] and a random DNA sequence was created in FASTQ format by XS simulator [11].…”