Advancing Genomics with OrthoDB, BUSCO, and the LEM Framework
Аутори
Kriventseva, EVManni, M.
Seppey, M.
Tegenfeldt, F.
Berkeley, M.
Kuznetsov, D.
Zdobnov, EM.
Остала ауторства
Morić, IvanaĐorđević, Valentina
Конференцијски прилог (Објављена верзија)
,
© 2023 Institute of Molecular Genetics and Genetic Engineering, University of Belgrade
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The rapid growth of genomics data necessitates continuous advancements in bioinformatics
tools. This presentation highlights the latest updates to our toolbox, including OrthoDB v11,
BUSCO v5, and the LEM benchmarking framework.
OrthoDB (https://www.orthodb.org) is a leading resource for gene orthology and
functional annotations across diverse eukaryotes, prokaryotes, and viruses. Orthology
facilitates precise bridging of gene function knowledge within the genomics sphere.
OrthoDB v11 encompasses over 100 million genes from 18,000 prokaryotes and nearly
2,000 eukaryotes, providing extensive species coverage. The open-source OrthoLoger
software (https://orthologer.ezlab.org) allows mapping of novel gene sets to precomputed
orthologs, linking them to relevant annotations.
BUSCO (https://busco.ezlab.org) serves as a standard tool for assessing the completeness
of genome assemblies, transcriptomes, and predicted gene sets, complementing
assembly contiguity measures like N50 val...ues. A spin-off of OrthoDB, BUSCO evaluates
the presence and coverage of marker genes, offering an evolutionarily-grounded
expectation of gene content completeness. BUSCO v5 now automatically selects the most
suitable dataset for evaluation, outperforming the popular CheckM tool. Its efficiency is
particularly evident in large eukaryotic genomes, and it is uniquely capable of assessing
both eukaryotic and prokaryotic species, making it applicable to metagenome-assembled
genomes of unknown origin.
The LEMMI (https://lemmi.ezlab.org) benchmarking framework, now in version 2, facilitates
informed software tool selection. This Live Evaluation of Methods (LEM) for Metagenome
Investigation uses a container-based approach for continuous benchmarking and effective
end-user distribution. The versatile framework can be extended to other procedures,
such as gene orthology inference with LEMOrtho (https://lemortho.ezlab.org). The LEM
benchmarking approach aims to become a community-driven effort, allowing developers
to showcase novel methods and users to access standardized, easy-to-use software. We
encourage researchers to apply this framework in their domain and welcome feedback.
Кључне речи:
genomics / genomes / orthologs / genes / continuous benchmarkingИзвор:
4th Belgrade Bioinformatics Conference, 2023, 4, 31-31Издавач:
- Belgrade : Institute of molecular genetics and genetic engineering
Напомена:
- Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 2023
Колекције
Институција/група
Institut za molekularnu genetiku i genetičko inženjerstvoTY - CONF AU - Kriventseva, EV AU - Manni, M. AU - Seppey, M. AU - Tegenfeldt, F. AU - Berkeley, M. AU - Kuznetsov, D. AU - Zdobnov, EM. PY - 2023 UR - https://belbi.bg.ac.rs/ UR - https://imagine.imgge.bg.ac.rs/handle/123456789/1966 AB - The rapid growth of genomics data necessitates continuous advancements in bioinformatics tools. This presentation highlights the latest updates to our toolbox, including OrthoDB v11, BUSCO v5, and the LEM benchmarking framework. OrthoDB (https://www.orthodb.org) is a leading resource for gene orthology and functional annotations across diverse eukaryotes, prokaryotes, and viruses. Orthology facilitates precise bridging of gene function knowledge within the genomics sphere. OrthoDB v11 encompasses over 100 million genes from 18,000 prokaryotes and nearly 2,000 eukaryotes, providing extensive species coverage. The open-source OrthoLoger software (https://orthologer.ezlab.org) allows mapping of novel gene sets to precomputed orthologs, linking them to relevant annotations. BUSCO (https://busco.ezlab.org) serves as a standard tool for assessing the completeness of genome assemblies, transcriptomes, and predicted gene sets, complementing assembly contiguity measures like N50 values. A spin-off of OrthoDB, BUSCO evaluates the presence and coverage of marker genes, offering an evolutionarily-grounded expectation of gene content completeness. BUSCO v5 now automatically selects the most suitable dataset for evaluation, outperforming the popular CheckM tool. Its efficiency is particularly evident in large eukaryotic genomes, and it is uniquely capable of assessing both eukaryotic and prokaryotic species, making it applicable to metagenome-assembled genomes of unknown origin. The LEMMI (https://lemmi.ezlab.org) benchmarking framework, now in version 2, facilitates informed software tool selection. This Live Evaluation of Methods (LEM) for Metagenome Investigation uses a container-based approach for continuous benchmarking and effective end-user distribution. The versatile framework can be extended to other procedures, such as gene orthology inference with LEMOrtho (https://lemortho.ezlab.org). The LEM benchmarking approach aims to become a community-driven effort, allowing developers to showcase novel methods and users to access standardized, easy-to-use software. We encourage researchers to apply this framework in their domain and welcome feedback. PB - Belgrade : Institute of molecular genetics and genetic engineering C3 - 4th Belgrade Bioinformatics Conference T1 - Advancing Genomics with OrthoDB, BUSCO, and the LEM Framework EP - 31 SP - 31 VL - 4 UR - https://hdl.handle.net/21.15107/rcub_imagine_1966 ER -
@conference{ author = "Kriventseva, EV and Manni, M. and Seppey, M. and Tegenfeldt, F. and Berkeley, M. and Kuznetsov, D. and Zdobnov, EM.", year = "2023", abstract = "The rapid growth of genomics data necessitates continuous advancements in bioinformatics tools. This presentation highlights the latest updates to our toolbox, including OrthoDB v11, BUSCO v5, and the LEM benchmarking framework. OrthoDB (https://www.orthodb.org) is a leading resource for gene orthology and functional annotations across diverse eukaryotes, prokaryotes, and viruses. Orthology facilitates precise bridging of gene function knowledge within the genomics sphere. OrthoDB v11 encompasses over 100 million genes from 18,000 prokaryotes and nearly 2,000 eukaryotes, providing extensive species coverage. The open-source OrthoLoger software (https://orthologer.ezlab.org) allows mapping of novel gene sets to precomputed orthologs, linking them to relevant annotations. BUSCO (https://busco.ezlab.org) serves as a standard tool for assessing the completeness of genome assemblies, transcriptomes, and predicted gene sets, complementing assembly contiguity measures like N50 values. A spin-off of OrthoDB, BUSCO evaluates the presence and coverage of marker genes, offering an evolutionarily-grounded expectation of gene content completeness. BUSCO v5 now automatically selects the most suitable dataset for evaluation, outperforming the popular CheckM tool. Its efficiency is particularly evident in large eukaryotic genomes, and it is uniquely capable of assessing both eukaryotic and prokaryotic species, making it applicable to metagenome-assembled genomes of unknown origin. The LEMMI (https://lemmi.ezlab.org) benchmarking framework, now in version 2, facilitates informed software tool selection. This Live Evaluation of Methods (LEM) for Metagenome Investigation uses a container-based approach for continuous benchmarking and effective end-user distribution. The versatile framework can be extended to other procedures, such as gene orthology inference with LEMOrtho (https://lemortho.ezlab.org). The LEM benchmarking approach aims to become a community-driven effort, allowing developers to showcase novel methods and users to access standardized, easy-to-use software. We encourage researchers to apply this framework in their domain and welcome feedback.", publisher = "Belgrade : Institute of molecular genetics and genetic engineering", journal = "4th Belgrade Bioinformatics Conference", title = "Advancing Genomics with OrthoDB, BUSCO, and the LEM Framework", pages = "31-31", volume = "4", url = "https://hdl.handle.net/21.15107/rcub_imagine_1966" }
Kriventseva, E., Manni, M., Seppey, M., Tegenfeldt, F., Berkeley, M., Kuznetsov, D.,& Zdobnov, EM.. (2023). Advancing Genomics with OrthoDB, BUSCO, and the LEM Framework. in 4th Belgrade Bioinformatics Conference Belgrade : Institute of molecular genetics and genetic engineering., 4, 31-31. https://hdl.handle.net/21.15107/rcub_imagine_1966
Kriventseva E, Manni M, Seppey M, Tegenfeldt F, Berkeley M, Kuznetsov D, Zdobnov E. Advancing Genomics with OrthoDB, BUSCO, and the LEM Framework. in 4th Belgrade Bioinformatics Conference. 2023;4:31-31. https://hdl.handle.net/21.15107/rcub_imagine_1966 .
Kriventseva, EV, Manni, M., Seppey, M., Tegenfeldt, F., Berkeley, M., Kuznetsov, D., Zdobnov, EM., "Advancing Genomics with OrthoDB, BUSCO, and the LEM Framework" in 4th Belgrade Bioinformatics Conference, 4 (2023):31-31, https://hdl.handle.net/21.15107/rcub_imagine_1966 .