Efficient and Quality-Optimized Metagenomic Pipeline Designed for Taxonomic Classification in Routine Microbiological Clinical Tests

Autor: Sylvie Buffet-Bataillon, Guillaume Rizk, Vincent Cattoir, Mohamed Sassi, Vincent Thibault, Jennifer Del Giudice, Jean-Pierre Gangneux

Publikováno v: Microorganisms, Vol 10, Iss 4, p 711 (2022)

Metagenomics analysis is now routinely used for clinical diagnosis in several diseases, and we need confidence in interpreting metagenomics analysis of microbiota. Particularly from the side of clinical microbiology, we consider that it would be a ma

Externí odkaz: https://doaj.org/article/8cfa7d62811248fa81631e1b98215492

Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software

Autor: Alexander Sczyrba, Peter Hofmann, Peter Belmann, David Koslicki, Stefan Janssen, Johannes Dröge, Ivan Gregor, Stephan Majda, Jessika Fiedler, Eik Dahms, Andreas Bremges, Adrian Fritz, Ruben Garrido-Oter, Tue Sparholt Jørgensen, Nicole Shapiro, Philip D. Blood, Alexey Gurevich, Yang Bai, Dmitrij Turaev, Matthew Z. DeMaere, Rayan Chikhi, Niranjan Nagarajan, Christopher Quince, Fernando Meyer, Monika Balvoit, Lars Hestbjerg Hansen, Søren J. Sørensen, Burton K. H. Chia, Bertrand Denis, Jeff L. Froula, Zhong Wang, Robert Egan, Dongwan Don Kang, Jeffrey J. Cook, Charles Deltel, Michael Beckstette, Claire Lemaitre, Pierre Peterlongo, Guillaume Rizk, Dominique Lavenier, Yu-Wei Wu, Steven W. Singer, Chirag Jain, Marc Strous, Heiner Klingenberg, Peter Meinicke, Michael Barton, Thomas Lingner, Hsin-Hung Lin, Yu-Chieh Liao, Genivaldo Gueiros Z. Silva, Daniel A. Cuevas, Robert A. Edwards, Surya Saha, Vitor C. Piro, Bernhard Y. Renard, Mihai Pop, Hans-Peter Klenk, Markus Göker, Nikos C. Kyrpides, Tanja Woyke, Julia A. Vorholt, Paul Schulze-Lefert, Edward M. Rubin, Aaron E. Darling, Thomas Rattei, Alice C. McHardy

Publikováno v: Nature Methods
Nature Methods, 2017, 14 (11), pp.1063-1071. ⟨10.1038/nmeth.4458⟩
Nature Methods, Nature Publishing Group, 2017, 14 (11), pp.1063-1071. ⟨10.1038/nmeth.4458⟩
Sczyrba, A, Hofmann, P, Belmann, P, Koslicki, D, Janssen, S, Droege, J, Gregor, I, Majda, S, Fiedler, J, Dahms, E, Bremges, A, Fritz, A, Garrido-Oter, R, Jorgensen, T S, Shapiro, N, Blood, P D, Gurevich, A, Bai, Y, Turaev, D, DeMaere, M Z, Chikhi, R, Nagarajan, N, Quince, C, Hansen, L H, Sorensen, S J, Chia, B KH, Denis, B, Froula, J L, Wang, Z L, Egan, R, Kang, D D, Cook, J J, Deltel, C, Beckstette, M, Lemaitre, C, Peterlongo, P, Rizk, G, Lavenier, D, Wu, Y-W, Singer, S W, Jain, C, Strous, M, Klingenberg, H, Meinicke, P, Barton, M, Lingner, T, Lin, H-H, Liao, Y-C, Silva, G G Z, Cuevas, D A, Edwards, R A, Saha, S, Piro, V C, Renard, B Y, Pop, M, Klenk, H-P, Goeker, M, Kyrpides, N, Woyke, T, Vorholt, J A, Schulze-Lefert, P, Rubin, E M, Darling, A E, Rattei, T & McHardy, A C 2017, ' Critical Assessment of Metagenome Interpretation− a benchmark of computational metagenomics software ', bioRxiv, pp. 99127 . https://doi.org/10.1101/099127

In metagenome analysis, computational methods for assembly, taxonomic profiling and binning are key components facilitating downstream biological data interpretation. However, a lack of consensus about benchmarking datasets and evaluation metrics com

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5b973ea1c302f40d8f61a7de08a748e8
https://hal.science/hal-01633525

De Novo NGS Data Compression

Autor: Guillaume Rizk, Dominique Lavenier, Claire Lemaitre, Erwan Drezen, Gaëtan Benoit

Publikováno v: Algorithms for Next-Generation Sequencing Data
Mourad Elloumi. Algorithms for Next-Generation Sequencing Data, Springer, pp.91-115, 2017, 978-3-319-59826-0. ⟨10.1007/978-3-319-59826-0_4⟩
Algorithms for Next-Generation Sequencing Data ISBN: 9783319598246

International audience; This chapter deals with the compression of genomic data without reference genomes. It presents various techniques which have been specifically developed to compress sequencing data in lossless or lossy modes. The chapter also

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::81737c37d9fcbaff8c8713b7532249c0
https://hal.science/hal-01633718/document

Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph

Autor: Thibault Dayris, Erwan Drezen, Gaëtan Benoit, Guillaume Rizk, Dominique Lavenier, Raluca Uricaru, Claire Lemaitre

Publikováno v: BMC Bioinformatics
BMC Bioinformatics, BioMed Central, 2015, 16 (1), ⟨10.1186/s12859-015-0709-7⟩
BMC Bioinformatics, 2015, 16 (1), ⟨10.1186/s12859-015-0709-7⟩

Background Data volumes generated by next-generation sequencing (NGS) technologies is now a major concern for both data storage and transmission. This triggered the need for more efficient methods than general purpose compression tools, such as the w

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f10104e4658711f2647a4c05904be313
https://hal.inria.fr/hal-01214682

DSK: k-mer counting with very low memory usage

Autor: Dominique Lavenier, Guillaume Rizk, Rayan Chikhi

Publikováno v: Bioinformatics
Bioinformatics, Oxford University Press (OUP), 2013, 29 (5), pp.652-653. ⟨10.1093/bioinformatics/btt020⟩
Bioinformatics, 2013, 29 (5), pp.652-653. ⟨10.1093/bioinformatics/btt020⟩

Summary: Counting all the k-mers (substrings of length k) in DNA/RNA sequencing reads is the preliminary step of many bioinformatics applications. However, state of the art k-mer counting methods require that a large data structure resides in memory.

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5eae449e8b98f0f3e1f0c46ae0504661
https://hal.archives-ouvertes.fr/hal-00778473/file/dsk_preprint.pdf