DOE JGI Metagenome Workflow
暂无分享,去创建一个
Marcel Huntemann | Rekha Seshadri | Emiley A. Eloe-Fadrosh | Natalia N. Ivanova | Supratim Mukherjee | Brian Bushnell | Alicia Clum | Simon Roux | Chris Daum | Brian Foster | Bryce Foster | Patrick P. Hajek | Neha Varghese | T.B.K. Reddy | Yuko Yoshinaga | Nikos C Kyrpides | I-Min A. Chen | Alex Copeland | Natalia N. Ivanova | N. Kyrpides | Y. Yoshinaga | R. Seshadri | I. Chen | A. Copeland | N. Varghese | C. Daum | S. Roux | E. Eloe-Fadrosh | Alicia Clum | Brian Foster | Supratim Mukherjee | Marcel Huntemann | Bryce Foster | T. Reddy | T. Reddy | R. O'Malley | Brian Bushnell | Patrick Hajek | Rekha Seshadri
[1] Norman R. Pace,et al. Specific Ribosomal DNA Sequences from Diverse Environmental Settings Correlate with Experimental Contaminants , 1998, Applied and Environmental Microbiology.
[2] Donovan H Parks,et al. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database , 2019, Bioinform..
[3] Ian Sillitoe,et al. CATH: expanding the horizons of structure-based functional annotations for genome sequences , 2018, Nucleic Acids Res..
[4] Peer Bork,et al. 20 years of the SMART protein domain annotation resource , 2017, Nucleic Acids Res..
[5] D C White,et al. Indigenous and contaminant microbes in ultradeep mines. , 2003, Environmental microbiology.
[6] Erin Beck,et al. TIGRFAMs and Genome Properties in 2013 , 2012, Nucleic Acids Res..
[7] P. Pevzner,et al. metaSPAdes: a new versatile metagenomic assembler. , 2017, Genome research.
[8] Jennifer Lu,et al. Improved metagenomic analysis with Kraken 2 , 2019, Genome Biology.
[9] I-Min A. Chen,et al. Genomes OnLine database (GOLD) v.7: updates and new features , 2018, Nucleic Acids Res..
[10] Connor T. Skennerton,et al. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes , 2015, Genome research.
[11] M. Frith,et al. Adaptive seeds tame genomic sequence comparison. , 2011, Genome research.
[12] C. Huttenhower,et al. Metagenomic microbial community profiling using unique clade-specific marker genes , 2012, Nature Methods.
[13] Patricia P. Chan,et al. tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences. , 2019, Methods in molecular biology.
[14] Kunihiko Sadakane,et al. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph , 2014, Bioinform..
[15] Natalia N. Ivanova,et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea , 2017, Nature Biotechnology.
[16] Robert D. Finn,et al. The Pfam protein families database: towards a more sustainable future , 2015, Nucleic Acids Res..
[17] Alex Copeland,et al. Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades , 2020, Environmental Microbiome.
[18] Sean R. Eddy,et al. Infernal 1.1: 100-fold faster RNA homology searches , 2013, Bioinform..
[19] William Arndt,et al. Modifying HMMER3 to Run Efficiently on the Cori Supercomputer Using OpenMP Tasking , 2018, 2018 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW).
[20] Torsten Seemann,et al. Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..
[21] Nikos Kyrpides,et al. CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats , 2007, BMC Bioinformatics.
[22] I-Min A. Chen,et al. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes , 2018, Nucleic Acids Res..
[23] I-Min A. Chen,et al. The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities , 2020, Nucleic Acids Res..
[24] Fernando Puente-Sánchez,et al. SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline , 2018, bioRxiv.
[25] Miriam L. Land,et al. Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .
[26] Robert D. Finn,et al. Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families , 2017, Nucleic Acids Res..
[27] Scott Federhen,et al. The NCBI Taxonomy database , 2011, Nucleic Acids Res..
[28] J. O’Hanlon,et al. Analysis of Bacteria Contaminating Ultrapure Water in Industrial Systems , 2002, Applied and Environmental Microbiology.
[29] Elizabeth M Glass,et al. MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function. , 2016, Methods in molecular biology.
[30] Robert D. Finn,et al. MGnify: the microbiome analysis resource in 2020 , 2019, Nucleic Acids Res..
[31] S. Eddy,et al. Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions , 2013, Nucleic acids research.
[32] C. Chothia,et al. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. , 2001, Journal of molecular biology.
[33] I-Min A. Chen,et al. Genomes OnLine Database (GOLD) v.8: overview and updates , 2020, Nucleic Acids Res..
[34] Luke R. Thompson,et al. Species-level functional profiling of metagenomes and metatranscriptomes , 2018, Nature Methods.
[35] Michael Y. Galperin,et al. Expanded microbial genome coverage and improved protein family annotation in the COG database , 2014, Nucleic Acids Res..
[36] Minoru Kanehisa,et al. KEGG: new perspectives on genomes, pathways, diseases and drugs , 2016, Nucleic Acids Res..
[37] Dongwan D. Kang,et al. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities , 2015, PeerJ.
[38] Paul Turner,et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses , 2014, BMC Biology.
[39] M. Borodovsky,et al. Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes , 2018, Genome research.