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Simulating Illumina metagenomic data with InSilicoSeq

Hadrien Gourlé, Oskar Karlsson-Lindsjö, Juliette Hayer, Erik Bongcam-Rudloff, John Hancock
2018 Bioinformatics  
InSilicoSeq is the only simulator that manages to simulate low-quality sequences.  ...  InSilicoSeq and ART are the most faithful to real data, while grinder only generates qualities of either "low" or "high" (Q10 and Q30 in our benchmarks). pIRS only reports Q40.  ... 
doi:10.1093/bioinformatics/bty630 pmid:30016412 fatcat:nwneebxtq5ecjhqmsw3zt6piwq

M&Ms: A software for building realistic Microbial Mock communities [article]

Natalia García-García, Javier Tamames, Fernando Puente-Sánchez
2021 bioRxiv   pre-print
Although there is a large amount of software dedicated to produce reads from 'in silico' microbial communities, often the simulated data diverge widely from real situations.ResultsHere, we introduce M&  ...  As these tools need to be tested, it is important to simulate datasets that resemble realistic conditions.  ...  Finally, M&Ms runs InSilicoSeqs (Gourlé et al., 2019) to simulate metagenomic Illumina sequencing samples with the designed abundance profiles.  ... 
doi:10.1101/2021.04.21.440404 fatcat:f4uuw5tg4rdkrfkbdjnyflfsea

Metagenomics: A viable tool for reconstructing herbivore diet

Physilia Y.S. Chua, Alex Crampton‐Platt, Youri Lammers, Inger G. Alsos, Sanne Boessenkool, Kristine Bohmann
2021 Molecular Ecology Resources  
Metagenomics can generate data on the diet of herbivores, without the need for primer selection and PCR enrichment steps as is necessary in metabarcoding.  ...  We applied these parameters to characterise the diet of western capercaillies (Tetrao urogallus) located in Norway, and compared the results with metabarcoding trnL P6 loop data generated from the same  ...  For each simulated data set, insilicoseq (using a precomputed error model based on a HiSeq instrument) generated around 1 million fragmented Illumina PE reads (125 bp).  ... 
doi:10.1111/1755-0998.13425 pmid:33971086 fatcat:zi7ggkoeivallcbm7z4gcojzra

Identification of discriminatory antibiotic resistance genes among environmental resistomes using extremely randomized tree algorithm

Suraj Gupta, Gustavo Arango-Argoty, Liqing Zhang, Amy Pruden, Peter Vikesland
2019 Microbiome  
The potential of ERT for identifying discriminatory ARGs was first evaluated using in silico metagenomic datasets (simulated metagenomic Illumina sequencing data) with known variability.  ...  The application of ERT was then demonstrated through analyses using publicly available and in-house metagenomic datasets associated with (1) different aquatic habitats (e.g., river, wastewater influent  ...  Acknowledgements We would like to thank Maria Virginia Riquelme and Emily Garner for their support in providing wastewater influent sample metagenomic datasets.  ... 
doi:10.1186/s40168-019-0735-1 pmid:31466530 pmcid:PMC6716844 fatcat:c7wutr4fdfgl3log5jbdeyetxe

Simulating metagenomic stable isotope probing datasets with MetaSIPSim

Samuel E. Barnett, Daniel H. Buckley
2020 BMC Bioinformatics  
MetaSIPSim allows for simulation of metagenomic-SIP datasets which facilitates the optimization and development of metagenomic-SIP experiments and analytical approaches for dealing with these data.  ...  To this end, we used MetaSIPSim generated data to demonstrate the advantages of metagenomic-SIP over a conventional shotgun metagenomic sequencing experiment.  ...  Authors' contributions DHB conceived of the project, SEB designed and wrote the software and conducted the analysis, SEB wrote the manuscript with input and edits from DHB.  ... 
doi:10.1186/s12859-020-3372-6 pmid:32000676 fatcat:vxmj7g7kdzfutpoddlqzktp75m

Simulating metagenomic stable isotope probing datasets with MetaSIPSim [article]

Samuel E Barnett, Daniel H Buckley
2019 bioRxiv   pre-print
MetaSIPSim allows for simulation of metagenomic-SIP datasets which facilitates the optimization and development of metagenomic-SIP experiments and analytical approaches for dealing with these data.  ...  To this end, we used MetaSIPSim generated data to demonstrate the advantages of metagenomic-SIP over a conventional shotgun metagenomic sequencing experiment.  ...  The error models are sequencing platform specific, with options for Illumina MiSeq, 222HiSeq, or NovaSeq. Unlike the original InSilicoSeq implementation, the MetaSIPSim script does 223 It .  ... 
doi:10.1101/735787 fatcat:qsis7bfg2rb6hbihdspqbbvdg4

Metagenomic Association Analysis of Gut Symbiont Limosilactobacillus reuteri Without Host-Specific Genome Isolation

Sein Park, Martin Steinegger, Ho-Seong Cho, Jongsik Chun
2020 Frontiers in Microbiology  
We observed not only the presence of host-specific lineages, but also the dominant lineages associated with the different hosts.  ...  We inferred evolutionary trajectories of host-associative L. reuteri strains in the metagenomic samples by placing the metagenome-assembled genomes into a phylogenetic tree and identified novel host-specific  ...  Validation With Simulated Metagenome Data Synthetic datasets were generated for three complexity levels from the L. reuteri reference genome sequences using InSilicoSeq v.1.3.5 (Gourle et al., 2019) :  ... 
doi:10.3389/fmicb.2020.585622 pmid:33329454 pmcid:PMC7717999 fatcat:6r2plaf54nej3jk5qekzyotv3i

Simulation study and comparative evaluation of viral contiguous sequence identification tools

Cody Glickman, Jo Hendrix, Michael Strong
2021 BMC Bioinformatics  
data.  ...  metagenomes with different read distributions, taxonomic compositions, and complexities.  ...  Simulated metagenomes were created using InSilicoSeq (version 1.2.0).  ... 
doi:10.1186/s12859-021-04242-0 pmid:34130621 fatcat:vtyuzrrh6bfonbt35g4zbewrte

Metagenomic association analysis of gut symbiont Lactobacillus reuteri without host-specific genome isolation [article]

Sein Park, Martin Steinegger, Ho-Seong Cho, Jongsik Chun
2020 bioRxiv   pre-print
We could observe not only the presence of host-specific lineages but also the dominant lineages associated with the different hosts.  ...  We could infer evolutionary trajectories of host-associative L. reuteri strains in the metagenomic samples by placing the metagenome-assembled genomes into a phylogenetic tree and identify novel host-specific  ...  Validation with simulated metagenome data We generated synthetic datasets for three complexity levels from the L. reuteri reference genome sequences using InSilicoSeq v1.  ... 
doi:10.1101/2020.05.19.101097 fatcat:6salecptg5gnlnoin4cn2n3ztm

Large scale microbiome profiling in the cloud

2019 Bioinformatics  
In this paper, we discuss a scalable, efficient and affordable approach to this problem, bringing big data solutions within the reach of laboratories with modest resources.  ...  Bacterial metagenomics profiling for metagenomic whole sequencing (mWGS) usually starts by aligning sequencing reads to a collection of reference genomes.  ...  Johnson and John Flynn at the Computer Science Department's IT Support group for their help with managing the reference genomes datasets, and to the members of the Bioinformatics Research Group (BioRG)  ... 
doi:10.1093/bioinformatics/btz356 pmid:31510682 pmcid:PMC6612844 fatcat:6nrieqwbprfexagctux26h3rau

META^2: Memory-efficient taxonomic classification and abundance estimation for metagenomics with deep learning [article]

Andreas Georgiou, Vincent Fortuin, Harun Mustafa, Gunnar Rätsch
2020 arXiv   pre-print
A task of particular interest is abundance estimation in metagenomic samples.  ...  Conventional read classification methods require large databases and vast amounts of memory to run, with recent deep learning methods suffering from very large model sizes.  ...  We simulate 151 bp error-free reads (default length of InSilicoSeq) used for training, while we generate more realistic reads with Illumina NovaSeq-type noise for validation and evaluation of our models  ... 
arXiv:1909.13146v2 fatcat:q4ya3ei3ifg7zk4vc2z7klmucm

Wochenende - modular and flexible alignment-based shotgun metagenome analysis [article]

Ilona Rosenboom, Fabian C Friedrich, Sophia Poertner, Marie-Madlen Pust, Tom Wehrbein, Bodo Rosenhahn, Lutz Wiehlmann, Patrick Chhatwal, Burkhard Tuemmler, Colin F Davenport
2022 bioRxiv   pre-print
Shotgun metagenome analysis provides a robust and verifiable method for comprehensive microbiome analysis of fungal, viral, archaeal and bacterial taxonomy, particularly with regard to visualization of  ...  Our novel normalization approach additionally allows calculation of absolute abundance profiles by comparison with reads assigned to the human host genome.  ...  grants from the Deutsche Forschungsgemeinschaft (SFB900, projects A2 and Z1, project no. 158989968), from the Volkswagen-Stiftung and the Niedersächsisches Ministerium für Wissenschaft und Kunst (Big Data  ... 
doi:10.1101/2022.03.18.484377 fatcat:67vtrienbncnbkdba57hu7vxya

A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing

Sergio Andreu-Sánchez, Lianmin Chen, Daoming Wang, Hannah E. Augustijn, Alexandra Zhernakova, Jingyuan Fu
2021 Frontiers in Genetics  
Our analysis of the simulated data shows that probabilistic method-based tools such as HaplotypeCaller and Mutect2 from the GATK toolset show the best performance.  ...  To do so, we simulated metagenomic reads to mimic human microbial composition, sequencing errors, and genetic variability.  ...  InSilicoSeq simulates reads using an error model based on Illumina's Hiseq technology.  ... 
doi:10.3389/fgene.2021.648229 pmid:34040632 pmcid:PMC8141913 fatcat:vs2q6xgav5dxxp2lq2ronm5eru

Improving metagenomic binning results with overlapped bins using assembly graphs

Vijini G Mallawaarachchi, Anuradha S Wickramarachchi, Yu Lin
2021 Algorithms for Molecular Biology  
In many metagenomics studies, the reads obtained from metagenomics sequencing are first assembled into longer contigs and these contigs are then binned into clusters of contigs where contigs in a cluster  ...  We show that GraphBin2 outperforms its predecessor GraphBin on both simulated and real datasets. GraphBin2 is freely available at https://github.com/Vini2/GraphBin2 .  ...  Acknowledgements This research was undertaken with the assistance of resources and services from the National Computational Infrastructure (NCI), which is supported by the Australian Government.  ... 
doi:10.1186/s13015-021-00185-6 pmid:33947431 fatcat:epi53xgm4vb3jghvesy46m5sg4

SCAPP: An algorithm for improved plasmid assembly in metagenomes [article]

David Pellow, Maraike Probst, Ori Furman, Alvah Zorea, Arik Segal, Itzik Mizrahi, Ron Shamir
2020 bioRxiv   pre-print
We compared performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome that we generated.  ...  We also created a parallel plasmidome-metagenome cow rumen sample and used it to create a novel assessment procedure.  ...  Paired-end short reads were simulated from the genome references using InSilicoSeq [7] with the HiSeq error model (default read length = 126bp).  ... 
doi:10.1101/2020.01.12.903252 fatcat:4qqjg6gvjbfpjdkjntcqlfbfim
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