ArticleBMC research notes2014
XS: a FASTQ read simulator.
Article in BMC research notes, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- A bioinformatics pipeline for a tick pathogen surveillance multiplex amplicon sequencing assay.Ticks and tick-borne diseases · 2023Article
- Boquila: NGS read simulator to eliminate read nucleotide bias in sequence analysis.Turkish journal of biology = Turk biyoloji dergisi · 2023Article
- A broad survey of DNA sequence data simulation tools.Briefings in functional genomics · 2020Review
- Next-generation forward genetic screens: using simulated data to improve the design of mapping-by-sequencing experiments in Arabidopsis.Nucleic acids research · 2019Article
- Article
- Comparison of Compression-Based Measures with Application to the Evolution of Primate Genomes.Entropy (Basel, Switzerland) · 2018Article
- AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework.PLoS computational biology · 2016Article
- A comparison of tools for the simulation of genomic next-generation sequencing data.Nature reviews. Genetics · 2016Review
- RNF: a general framework to evaluate NGS read mappers.Bioinformatics (Oxford, England) · 2016Article
- An alignment-free method to find and visualise rearrangements between pairs of DNA sequences.Scientific reports · 2015Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
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/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.