MeSS and Assembly_finder: a Toolkit for in Silico Metagenomic Sample Generation

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2024 Dec 31

PMID 39739308

Authors

Farid Chaabane

Trestan Pillonel

Claire Bertelli

Affiliations

Soon will be listed here.

Abstract

Summary: The intrinsic complexity of the microbiota combined with technical variability render shotgun metagenomics challenging to analyze for routine clinical or research applications. In silico data generation offers a controlled environment allowing for example to benchmark bioinformatics tools, to optimize study design, statistical power, or to validate targeted applications. Here, we propose assembly_finder and the Metagenomic Sequence Simulator (MeSS), two easy-to-use Bioconda packages, as part of a benchmarking toolkit to download genomes and simulate shotgun metagenomics samples, respectively. Outperforming existing tools in speed while requiring less memory, MeSS reproducibly generates accurate complex communities based on a list of taxonomic ranks and their abundance.

Availability And Implementation: All code is released under MIT License and is available on https://github.com/metagenlab/MeSS and https://github.com/metagenlab/assembly_finder.

References

Manni M, Berkeley M, Seppey M, Zdobnov E . BUSCO: Assessing Genomic Data Quality and Beyond. Curr Protoc. 2021; 1(12):e323. DOI: 10.1002/cpz1.323. View

Rong R, Jiang S, Xu L, Xiao G, Xie Y, Liu D . MB-GAN: Microbiome Simulation via Generative Adversarial Network. Gigascience. 2021; 10(2). PMC: 7931821. DOI: 10.1093/gigascience/giab005. View

. Structure, function and diversity of the healthy human microbiome. Nature. 2012; 486(7402):207-14. PMC: 3564958. DOI: 10.1038/nature11234. View

Caro H, Dollin S, Biton A, Brancotte B, Desvillechabrol D, Dufresne Y . BioConvert: a comprehensive format converter for life sciences. NAR Genom Bioinform. 2023; 5(3):lqad074. PMC: 10440784. DOI: 10.1093/nargab/lqad074. View

Federhen S . The NCBI Taxonomy database. Nucleic Acids Res. 2011; 40(Database issue):D136-43. PMC: 3245000. DOI: 10.1093/nar/gkr1178. View

Manni M, Berkeley M, Seppey M, Simao F, Zdobnov E . BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Mol Biol Evol. 2021; 38(10):4647-4654. PMC: 8476166. DOI: 10.1093/molbev/msab199. View

Huang W, Li L, Myers J, Marth G . ART: a next-generation sequencing read simulator. Bioinformatics. 2011; 28(4):593-4. PMC: 3278762. DOI: 10.1093/bioinformatics/btr708. View

Shen W, Le S, Li Y, Hu F . SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLoS One. 2016; 11(10):e0163962. PMC: 5051824. DOI: 10.1371/journal.pone.0163962. View

Roach M, Pierce-Ward N, Suchecki R, Mallawaarachchi V, Papudeshi B, Handley S . Ten simple rules and a template for creating workflows-as-applications. PLoS Comput Biol. 2022; 18(12):e1010705. PMC: 9754251. DOI: 10.1371/journal.pcbi.1010705. View

10.

Numanagic I, Bonfield J, Hach F, Voges J, Ostermann J, Alberti C . Comparison of high-throughput sequencing data compression tools. Nat Methods. 2016; 13(12):1005-1008. DOI: 10.1038/nmeth.4037. View

11.

Meyer F, Fritz A, Deng Z, Koslicki D, Lesker T, Gurevich A . Critical Assessment of Metagenome Interpretation: the second round of challenges. Nat Methods. 2022; 19(4):429-440. PMC: 9007738. DOI: 10.1038/s41592-022-01431-4. View

12.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N . The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. PMC: 2723002. DOI: 10.1093/bioinformatics/btp352. View

13.

OLeary N, Wright M, Brister J, Ciufo S, Haddad D, McVeigh R . Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 2015; 44(D1):D733-45. PMC: 4702849. DOI: 10.1093/nar/gkv1189. View

14.

Wood D, Lu J, Langmead B . Improved metagenomic analysis with Kraken 2. Genome Biol. 2019; 20(1):257. PMC: 6883579. DOI: 10.1186/s13059-019-1891-0. View

15.

Stephens Z, Hudson M, Mainzer L, Taschuk M, Weber M, Iyer R . Simulating Next-Generation Sequencing Datasets from Empirical Mutation and Sequencing Models. PLoS One. 2016; 11(11):e0167047. PMC: 5125660. DOI: 10.1371/journal.pone.0167047. View

16.

Gourle H, Karlsson-Lindsjo O, Hayer J, Bongcam-Rudloff E . Simulating Illumina metagenomic data with InSilicoSeq. Bioinformatics. 2018; 35(3):521-522. PMC: 6361232. DOI: 10.1093/bioinformatics/bty630. View

17.

Techtmann S, Hazen T . Metagenomic applications in environmental monitoring and bioremediation. J Ind Microbiol Biotechnol. 2016; 43(10):1345-54. DOI: 10.1007/s10295-016-1809-8. View

18.

Fritz A, Hofmann P, Majda S, Dahms E, Droge J, Fiedler J . CAMISIM: simulating metagenomes and microbial communities. Microbiome. 2019; 7(1):17. PMC: 6368784. DOI: 10.1186/s40168-019-0633-6. View

19.

Belmann P, Droge J, Bremges A, McHardy A, Sczyrba A, Barton M . Bioboxes: standardised containers for interchangeable bioinformatics software. Gigascience. 2015; 4:47. PMC: 4607242. DOI: 10.1186/s13742-015-0087-0. View

20.

Scherz V, Greub G, Bertelli C . Building up a clinical microbiota profiling: a quality framework proposal. Crit Rev Microbiol. 2021; 48(3):356-375. DOI: 10.1080/1040841X.2021.1975642. View