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Simulating Illumina metagenomic data with InSilicoSeq
2018
Bioinformatics
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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]
2021
bioRxiv
pre-print
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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
2021
Molecular Ecology Resources
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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
2019
Microbiome
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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
2020
BMC Bioinformatics
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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]
2019
bioRxiv
pre-print
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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
2020
Frontiers in Microbiology
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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
2021
BMC Bioinformatics
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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]
2020
bioRxiv
pre-print
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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
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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]
2020
arXiv
pre-print
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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]
2022
bioRxiv
pre-print
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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
2021
Frontiers in Genetics
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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
2021
Algorithms for Molecular Biology
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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]
2020
bioRxiv
pre-print
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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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