ArticlePloS one2013
NeSSM: a Next-generation Sequencing Simulator for Metagenomics.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
38 citing papers in PubMed.
- Semisynthetic simulation for microbiome data analysis.Briefings in bioinformatics · 2024Review
- Simulated High Throughput Sequencing Datasets: A Crucial Tool for Validating Bioinformatic Pathogen Detection Pipelines.Biology · 2024Article
- SWAMPy: simulating SARS-CoV-2 wastewater amplicon metagenomes.Bioinformatics (Oxford, England) · 2024Article
- Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis.International journal of molecular sciences · 2024Review
- Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim.GigaScience · 2023Article
- Boquila: NGS read simulator to eliminate read nucleotide bias in sequence analysis.Turkish journal of biology = Turk biyoloji dergisi · 2023Article
- Phylogeny analysis of whole protein-coding genes in metagenomic data detected an environmental gradient for the microbiota.PloS one · 2023Article
- Article
- Genome sequence assembly algorithms and misassembly identification methods.Molecular biology reports · 2022Review
- Article
- Prediction and analysis of metagenomic operons via MetaRon: a pipeline for prediction of Metagenome and whole-genome opeRons.BMC genomics · 2021Article
- Reads Binning Improves the Assembly of Viral Genome Sequences From Metagenomic Samples.Frontiers in microbiology · 2021Article
- SimuSCoP: reliably simulate Illumina sequencing data based on position and context dependent profiles.BMC bioinformatics · 2020Article
- A broad survey of DNA sequence data simulation tools.Briefings in functional genomics · 2020Review
- Article
- Biochemical Characteristics of Microbial Enzymes and Their Significance from Industrial Perspectives.Molecular biotechnology · 2019Review
- CAMISIM: simulating metagenomes and microbial communities.Microbiome · 2019Article
- Simulating Illumina metagenomic data with InSilicoSeq.Bioinformatics (Oxford, England) · 2019Article
- Using QC-Blind for Quality Control and Contamination Screening of Bacteria DNA Sequencing Data Without Reference Genome.Frontiers in microbiology · 2019Article
- Reads Binning Improves Alignment-Free Metagenome Comparison.Frontiers in genetics · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMetagenomics can reveal the vast majority of microbes that have been missed by traditional cultivation-based methods. Due to its extremely wide range of application areas, fast metagenome sequencing simulation systems with high fidelity are in great demand to facilitate the development and comparison of metagenomics analysis tools.
resultsWe present here a customizable metagenome simulation system: NeSSM (Next-generation Sequencing Simulator for Metagenomics). Combining complete genomes currently available, a community composition table, and sequencing parameters, it can simulate metagenome sequencing better than existing systems. Sequencing error models based on the explicit distribution of errors at each base and sequencing coverage bias are incorporated in the simulation. In order to improve the fidelity of simulation, tools are provided by NeSSM to estimate the sequencing error models, sequencing coverage bias and the community composition directly from existing metagenome sequencing data. Currently, NeSSM supports single-end and pair-end sequencing for both 454 and Illumina platforms. In addition, a GPU (graphics processing units) version of NeSSM is also developed to accelerate the simulation. By comparing the simulated sequencing data from NeSSM with experimental metagenome sequencing data, we have demonstrated that NeSSM performs better in many aspects than existing popular metagenome simulators, such as MetaSim, GemSIM and Grinder. The GPU version of NeSSM is more than one-order of magnitude faster than MetaSim.
conclusionsNeSSM is a fast simulation system for high-throughput metagenome sequencing. It can be helpful to develop tools and evaluate strategies for metagenomics analysis and it's freely available for academic users at http://cbb.sjtu.edu.cn/~ccwei/pub/software/NeSSM.php.
Indexed as
Identifiers
What OpenQuestion holds
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.