DOE JGI Metagenome Workflow.
作者： Nikos C. Kyrpides , Supratim Mukherjee , Alicia Clum , Natalia N. Ivanova , Rekha Seshadri
DOI: 10.1128/MSYSTEMS.00804-20
关键词: Metagenomics 、 Annotation 、 Data pre-processing 、 Workflow 、 Genomes OnLine Database 、 Set (abstract data type) 、 FASTQ format 、 Metadata 、 Information retrieval 、 Computer science
摘要: … of data processing. The workflow modules for read filtering and metagenome assembly are … require filling out the project and associated metadata descriptions in the Genomes OnLine …
sci-hub.st 参考文章(37)
Dongwan D. Kang, Jeff Froula, Rob Egan, Zhong Wang, MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities PeerJ. ,vol. 3, ,(2015) , 10.7717/PEERJ.1165
Daniel H. Haft, Jeremy D. Selengut, Roland A. Richter, Derek Harkins, Malay K. Basu, Erin Beck, TIGRFAMs and Genome Properties in 2013 Nucleic Acids Research. ,vol. 41, pp. 387- 395 ,(2012) , 10.1093/NAR/GKS1234
T. Seemann, Prokka: Rapid Prokaryotic Genome Annotation Bioinformatics. ,vol. 30, pp. 2068- 2069 ,(2014) , 10.1093/BIOINFORMATICS/BTU153
Julian Gough, Kevin Karplus, Richard Hughey, Cyrus Chothia, Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. Journal of Molecular Biology. ,vol. 313, pp. 903- 919 ,(2001) , 10.1006/JMBI.2001.5080
Jaina Mistry, Robert D. Finn, Sean R. Eddy, Alex Bateman, Marco Punta, Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions Nucleic Acids Research. ,vol. 41, ,(2013) , 10.1093/NAR/GKT263
Leonid A. Kulakov, Morven B. McAlister, Kimberly L. Ogden, Michael J. Larkin, John F. O'Hanlon, Analysis of Bacteria Contaminating Ultrapure Water in Industrial Systems Applied and Environmental Microbiology. ,vol. 68, pp. 1548- 1555 ,(2002) , 10.1128/AEM.68.4.1548-1555.2002
Donovan H. Parks, Michael Imelfort, Connor T. Skennerton, Philip Hugenholtz, Gene W. Tyson, CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Genome Research. ,vol. 25, pp. 1043- 1055 ,(2015) , 10.1101/GR.186072.114
Dinghua Li, Chi-Man Liu, Ruibang Luo, Kunihiko Sadakane, Tak-Wah Lam, MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph Bioinformatics. ,vol. 31, pp. 1674- 1676 ,(2015) , 10.1093/BIOINFORMATICS/BTV033
Charles Bland, Teresa L Ramsey, Fareedah Sabree, Micheal Lowe, Kyndall Brown, Nikos C Kyrpides, Philip Hugenholtz, CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. ,vol. 8, pp. 209- 209 ,(2007) , 10.1186/1471-2105-8-209
Nicola Segata, Levi Waldron, Annalisa Ballarini, Vagheesh Narasimhan, Olivier Jousson, Curtis Huttenhower, Metagenomic microbial community profiling using unique clade-specific marker genes. Nature Methods. ,vol. 9, pp. 811- 814 ,(2012) , 10.1038/NMETH.2066