MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs

Autor: Daniel H. Huson, Benjamin Albrecht, Caner Bağcı, Irina Bessarab, Anna Górska, Dino Jolic, Rohan B. H. Williams

Publikováno v: Biology Direct, Vol 13, Iss 1, Pp 1-17 (2018)

Abstract Background There are numerous computational tools for taxonomic or functional analysis of microbiome samples, optimized to run on hundreds of millions of short, high quality sequencing reads. Programs such as MEGAN allow the user to interact

Externí odkaz: https://doaj.org/article/74967af252c749e0983e6a72f7fddd37

Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function

Autor: Terrance P. Snutch, Spyridon Oikonomopoulos, Tue Kjærgaard Nielsen, Miten Jain, Eric van der Helm, Richard M. Leggett, Dino Jolic, Hollian Richardson, Justin O'Grady, Hans J. Jansen, Jiannis Ragoussis, Ned Peel, David Eccles, Devin M. Drown, Lars Hestbjerg Hansen, Thomas Barry, John R. Tyson, Anne-Lise Ducluzeau, Bonnie L. Brown, Anthony Bayega, Kate Reddington, Darren Heavens

Publikováno v: Reddington, K, Eccles, D, O'Grady, J, Drown, D M, Hansen, L H, Nielsen, T K, Ducluzeau, A L, Leggett, R M, Heavens, D, Peel, N, Snutch, T P, Bayega, A, Oikonomopoulos, S, Ragoussis, J, Barry, T, van der Helm, E, Jolic, D, Richardson, H, Jansen, H, Tyson, J R, Jain, M & Brown, B L 2020, ' Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function ', GigaScience, vol. 9, no. 6, giaa053 . https://doi.org/10.1093/gigascience/giaa053
Reddington, K, Eccles, D, O'Grady, J, Drown, D M, Hansen, L H, Nielsen, T K, Ducluzeau, A-L, Leggett, R M, Heavens, D, Peel, N, Snutch, T P, Bayega, A, Oikonomopoulos, S, Ragoussis, J, Barry, T, van der Helm, E, Jolic, D, Richardson, H, Jansen, H, Tyson, J R, Jain, M & Brown, B L 2020, ' Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function ', GigaScience, vol. 9, no. 6, 053 . https://doi.org/10.1093/gigascience/giaa053
Reddington, K, Eccles, D, O'Grady, J, Drown, D M, Hansen, L H, Nielsen, T K, Ducluzeau, A L, Leggett, R M, Heavens, D, Peel, N, Snutch, T P, Bayega, A, Oikonomopoulos, S, Ragoussis, I, Barry, T, van der Helm, E, Jolic, D, Richardson, H, Jansen, H, Tyson, J R, Jain, M & Brown, B L 2020, ' Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function ', GigaScience, vol. 9, no. 6, giaa053 . https://doi.org/10.1093/gigascience/giaa053

Background Riverine ecosystems are biogeochemical powerhouses driven largely by microbial communities that inhabit water columns and sediments. Because rivers are used extensively for anthropogenic purposes (drinking water, recreation, agriculture, a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9cb7f41189bf05d654da37b7b0fa9ab2
https://orbit.dtu.dk/en/publications/503cff13-37a3-40e7-ac13-683a2ac694b3

ONT Library Preparation v1

Autor: Kate Reddington, David Eccles, Justin O’Grady, Devin M. Drown, Lars Hestbjerg Hansen, Tue Kjærgaard Nielsen, Anne-Lise Ducluzeau, Richard M. Leggett, Darren Heavens, Ned Peel, Terrance P. Snutch, Anthony Bayega, Spyros Oikonomopoulos, Jiannis Ragoussis, Thomas Barry, Eric van der Helm, Dino Jolic, Hollian Richardson, Hans Jansen, John R. Tyson, Miten Jain, Bonnie L. Brown

Newly released Rapid Low Input by PCR Barcoding Sequencing Kit (SQK-RLB001); minor adjustments indicated by (*).

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::961a1487f7b8460e7ea9100d5fe7c3ce
https://doi.org/10.17504/protocols.io.qwcdxaw

Linking Genomic and Metabolomic Natural Variation Uncovers Nematode Pheromone Biosynthesis

Autor: Gabriel V. Markov, Dino Jolic, Dominik G. Grimm, Oishika Panda, Ying K. Zhang, Ralf J. Sommer, Frank C. Schroeder, Henry H. Le, Alexander B. Artyukhin, Joshua J. Yim, Christian Rödelsperger, Marc H. Claassen, Jan M. Falcke, Joshua A. Baccile, Neelanjan Bose

Publikováno v: Cell chemical biology. 25(6)

Summary In the nematodes Caenorhabditis elegans and Pristionchus pacificus, a modular library of small molecules control behavior, lifespan, and development. However, little is known about the final steps of their biosynthesis, in which diverse build

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3ef63c15816fb7b6e0db66139d4d3c42
https://pubmed.ncbi.nlm.nih.gov/29779955