Metagenome-assembled genome extraction and analysis from microbiomes using KBase
Abstract
Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only become possible recently. In order to realize the hope of capturing Earth’s microbial genetic complement and to facilitate the investigation of the functional roles of specific lineages in a given ecosystem, technologies that accelerate the recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high-quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). Overall, these steps take about a day to obtain extracted genomes when starting from smaller environmental shotgun read libraries, or up to about a week from larger libraries. In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAGs, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq and others. While portions of such capabilities are available individually from other resources, the combination of the intuitive usability, data interoperability and integration of tools in a freely available computationalmore »
- Authors:
-
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
- Argonne National Lab. (ANL), Lemont, IL (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Predicine, Inc., Hayward, CA (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Google, Inc., San Francisco, CA (United States)
- Univ. of Tennessee, Knoxville, TN (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1899026
- Grant/Contract Number:
- AC05-00OR22725; AC02-05CH11231; AC02-06CH11357; AC02-98CH10886
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Protocols
- Additional Journal Information:
- Journal Volume: 18; Journal Issue: 11; Journal ID: ISSN 1754-2189
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; bioinformatics; genome assembly algorithms; metagenomics; microbial ecology; microbiology techniques
Citation Formats
Chivian, Dylan, Jungbluth, Sean P., Dehal, Paramvir S., Wood-Charlson, Elisha M., Canon, Richard S., Allen, Benjamin H., Clark, Mikayla M., Gu, Tianhao, Land, Miriam L., Price, Gavin A., Riehl, William J., Sneddon, Michael W., Sutormin, Roman, Zhang, Qizhi, Cottingham, Jr., Robert W., Henry, Chris S., and Arkin, Adam P. Metagenome-assembled genome extraction and analysis from microbiomes using KBase. United States: N. p., 2022.
Web. doi:10.1038/s41596-022-00747-x.
Chivian, Dylan, Jungbluth, Sean P., Dehal, Paramvir S., Wood-Charlson, Elisha M., Canon, Richard S., Allen, Benjamin H., Clark, Mikayla M., Gu, Tianhao, Land, Miriam L., Price, Gavin A., Riehl, William J., Sneddon, Michael W., Sutormin, Roman, Zhang, Qizhi, Cottingham, Jr., Robert W., Henry, Chris S., & Arkin, Adam P. Metagenome-assembled genome extraction and analysis from microbiomes using KBase. United States. https://doi.org/10.1038/s41596-022-00747-x
Chivian, Dylan, Jungbluth, Sean P., Dehal, Paramvir S., Wood-Charlson, Elisha M., Canon, Richard S., Allen, Benjamin H., Clark, Mikayla M., Gu, Tianhao, Land, Miriam L., Price, Gavin A., Riehl, William J., Sneddon, Michael W., Sutormin, Roman, Zhang, Qizhi, Cottingham, Jr., Robert W., Henry, Chris S., and Arkin, Adam P. Mon .
"Metagenome-assembled genome extraction and analysis from microbiomes using KBase". United States. https://doi.org/10.1038/s41596-022-00747-x. https://www.osti.gov/servlets/purl/1899026.
@article{osti_1899026,
title = {Metagenome-assembled genome extraction and analysis from microbiomes using KBase},
author = {Chivian, Dylan and Jungbluth, Sean P. and Dehal, Paramvir S. and Wood-Charlson, Elisha M. and Canon, Richard S. and Allen, Benjamin H. and Clark, Mikayla M. and Gu, Tianhao and Land, Miriam L. and Price, Gavin A. and Riehl, William J. and Sneddon, Michael W. and Sutormin, Roman and Zhang, Qizhi and Cottingham, Jr., Robert W. and Henry, Chris S. and Arkin, Adam P.},
abstractNote = {Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only become possible recently. In order to realize the hope of capturing Earth’s microbial genetic complement and to facilitate the investigation of the functional roles of specific lineages in a given ecosystem, technologies that accelerate the recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high-quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). Overall, these steps take about a day to obtain extracted genomes when starting from smaller environmental shotgun read libraries, or up to about a week from larger libraries. In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAGs, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq and others. While portions of such capabilities are available individually from other resources, the combination of the intuitive usability, data interoperability and integration of tools in a freely available computational resource makes KBase a powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended with additional MAG recovery and analysis tools, via the KBase software development kit (SDK).},
doi = {10.1038/s41596-022-00747-x},
journal = {Nature Protocols},
number = 11,
volume = 18,
place = {United States},
year = {Mon Nov 14 00:00:00 EST 2022},
month = {Mon Nov 14 00:00:00 EST 2022}
}
Works referenced in this record:
Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes
journal, July 2019
- Bertrand, Denis; Shaw, Jim; Kalathiyappan, Manesh
- Nature Biotechnology, Vol. 37, Issue 8
Accurate read-based metagenome characterization using a hierarchical suite of unique signatures
journal, March 2015
- Freitas, Tracey Allen K.; Li, Po-E; Scholz, Matthew B.
- Nucleic Acids Research, Vol. 43, Issue 10
QUAST: quality assessment tool for genome assemblies
journal, February 2013
- Gurevich, Alexey; Saveliev, Vladislav; Vyahhi, Nikolay
- Bioinformatics, Vol. 29, Issue 8
DRAM for distilling microbial metabolism to automate the curation of microbiome function
journal, August 2020
- Shaffer, Michael; Borton, Mikayla A.; McGivern, Bridget B.
- Nucleic Acids Research, Vol. 48, Issue 16
Cutadapt removes adapter sequences from high-throughput sequencing reads
journal, May 2011
- Martin, Marcel
- EMBnet.journal, Vol. 17, Issue 1
microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes
journal, July 2022
- Karaoz, Ulas; Brodie, Eoin L.
- Frontiers in Bioinformatics, Vol. 2
Improved metagenomic analysis with Kraken 2
journal, November 2019
- Wood, Derrick E.; Lu, Jennifer; Langmead, Ben
- Genome Biology, Vol. 20, Issue 1
Globus Online: Accelerating and Democratizing Science through Cloud-Based Services
journal, May 2011
- Foster, Ian
- IEEE Internet Computing, Vol. 15, Issue 3
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
journal, August 2017
- Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas
- Nature Biotechnology, Vol. 35, Issue 8
Accurate and complete genomes from metagenomes
journal, March 2020
- Chen, Lin-Xing; Anantharaman, Karthik; Shaiber, Alon
- Genome Research, Vol. 30, Issue 3
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation
journal, May 2018
- Zhang, Han; Yohe, Tanner; Huang, Le
- Nucleic Acids Research, Vol. 46, Issue W1
Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets
journal, September 2021
- Youngblut, Nicholas D.; Ley, Ruth E.
- PeerJ, Vol. 9
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
journal, September 2020
- Seaver, Samuel M. D.; Liu, Filipe; Zhang, Qizhi
- Nucleic Acids Research, Vol. 49, Issue D1
Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements
journal, June 2004
- Darling, A. C. E.
- Genome Research, Vol. 14, Issue 7
The GenePattern Notebook Environment
journal, August 2017
- Reich, Michael; Tabor, Thorin; Liefeld, Ted
- Cell Systems, Vol. 5, Issue 2
Trimmomatic: a flexible trimmer for Illumina sequence data
journal, April 2014
- Bolger, Anthony M.; Lohse, Marc; Usadel, Bjoern
- Bioinformatics, Vol. 30, Issue 15
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center
journal, November 2016
- Wattam, Alice R.; Davis, James J.; Assaf, Rida
- Nucleic Acids Research, Vol. 45, Issue D1
TIGRFAMs and Genome Properties in 2013
journal, November 2012
- Haft, Daniel H.; Selengut, Jeremy D.; Richter, Roland A.
- Nucleic Acids Research, Vol. 41, Issue D1
GenBank
journal, November 2017
- Benson, Dennis A.; Cavanaugh, Mark; Clark, Karen
- Nucleic Acids Research, Vol. 46, Issue D1
Database resources of the National Center for Biotechnology Information
journal, October 2020
- Sayers, Eric W.; Beck, Jeffrey; Bolton, Evan E.
- Nucleic Acids Research, Vol. 49, Issue D1
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
journal, January 2015
- Li, Dinghua; Liu, Chi-Man; Luo, Ruibang
- Bioinformatics, Vol. 31, Issue 10
A Comparison of Microbial Genome Web Portals
journal, February 2019
- Karp, Peter D.; Ivanova, Natalia; Krummenacker, Markus
- Frontiers in Microbiology, Vol. 10
SciApps
conference, July 2018
- Wang, Liya; Lu, Zhenyuan; Buren, Peter Van
- Proceedings of the Practice and Experience on Advanced Research Computing
EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
journal, May 2011
- Miller, Christopher S.; Baker, Brett J.; Thomas, Brian C.
- Genome Biology, Vol. 12, Issue 5
The Earth Microbiome project: successes and aspirations
journal, August 2014
- Gilbert, Jack A.; Jansson, Janet K.; Knight, Rob
- BMC Biology, Vol. 12, Issue 1
RefSeq: an update on prokaryotic genome annotation and curation
journal, November 2017
- Haft, Daniel H.; DiCuccio, Michael; Badretdin, Azat
- Nucleic Acids Research, Vol. 46, Issue D1
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
journal, March 2010
- Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P.
- PLoS ONE, Vol. 5, Issue 3
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update
journal, May 2016
- Afgan, Enis; Baker, Dannon; van den Beek, Marius
- Nucleic Acids Research, Vol. 44, Issue W1
metaSPAdes: a new versatile metagenomic assembler
journal, March 2017
- Nurk, Sergey; Meleshko, Dmitry; Korobeynikov, Anton
- Genome Research, Vol. 27, Issue 5
Terabase-scale metagenome coassembly with MetaHipMer
journal, July 2020
- Hofmeyr, Steven; Egan, Rob; Georganas, Evangelos
- Scientific Reports, Vol. 10, Issue 1
Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010
- Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F.
- BMC Bioinformatics, Vol. 11, Issue 1
Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets
journal, July 2020
- Yue, Yi; Huang, Hao; Qi, Zhao
- BMC Bioinformatics, Vol. 21, Issue 1
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
journal, October 2015
- Wu, Yu-Wei; Simmons, Blake A.; Singer, Steven W.
- Bioinformatics, Vol. 32, Issue 4
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
journal, August 2018
- Parks, Donovan H.; Chuvochina, Maria; Waite, David W.
- Nature Biotechnology, Vol. 36, Issue 10
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
journal, May 2015
- Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T.
- Genome Research, Vol. 25, Issue 7
Interactive metagenomic visualization in a Web browser
journal, September 2011
- Ondov, Brian D.; Bergman, Nicholas H.; Phillippy, Adam M.
- BMC Bioinformatics, Vol. 12, Issue 1
Fast and sensitive taxonomic classification for metagenomics with Kaiju
journal, April 2016
- Menzel, Peter; Ng, Kim Lee; Krogh, Anders
- Nature Communications, Vol. 7, Issue 1
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
journal, September 2003
- Li, L.
- Genome Research, Vol. 13, Issue 9
Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust
journal, June 2013
- Rajeev, Lara; da Rocha, Ulisses Nunes; Klitgord, Niels
- The ISME Journal, Vol. 7, Issue 11
Moab Desert Crust - Sample 4E
dataset, January 2021
- Chivian, Dylan; Jungbluth, Sean; Dehal, Paramvir
- U.S. Department of Energy Systems Biology Knowledgebase
A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum.
journal, December 2021
- Kumari, Sunita; Kumar, Vivek; Beilsmith, Kathleen
- Current Plant Biology, Vol. 28
MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis
journal, September 2018
- Uritskiy, Gherman V.; DiRuggiero, Jocelyne; Taylor, James
- Microbiome, Vol. 6, Issue 1
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
journal, March 1998
- Ewing, Brent; Green, Phil
- Genome Research, Vol. 8, Issue 3
metaMicrobesOnline: phylogenomic analysis of microbial communities
journal, November 2012
- Chivian, Dylan; Dehal, Paramvir S.; Keller, Keith
- Nucleic Acids Research, Vol. 41, Issue D1
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy
journal, May 2018
- Sieber, Christian M. K.; Probst, Alexander J.; Sharrar, Allison
- Nature Microbiology, Vol. 3, Issue 7
Expanded microbial genome coverage and improved protein family annotation in the COG database
journal, November 2014
- Galperin, Michael Y.; Makarova, Kira S.; Wolf, Yuri I.
- Nucleic Acids Research, Vol. 43, Issue D1
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
journal, April 2012
- Peng, Y.; Leung, H. C. M.; Yiu, S. M.
- Bioinformatics, Vol. 28, Issue 11
Prokka: rapid prokaryotic genome annotation
journal, March 2014
- Seemann, T.
- Bioinformatics, Vol. 30, Issue 14
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy
journal, September 2021
- Parks, Donovan H.; Chuvochina, Maria; Rinke, Christian
- Nucleic Acids Research, Vol. 50, Issue D1
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
journal, January 2019
- Pasolli, Edoardo; Asnicar, Francesco; Manara, Serena
- Cell, Vol. 176, Issue 3
KBase: The United States Department of Energy Systems Biology Knowledgebase
journal, July 2018
- Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S.
- Nature Biotechnology, Vol. 36, Issue 7
The Pfam protein families database in 2019
journal, October 2018
- El-Gebali, Sara; Mistry, Jaina; Bateman, Alex
- Nucleic Acids Research, Vol. 47, Issue D1
A method for achieving complete microbial genomes and improving bins from metagenomics data
journal, May 2021
- Lui, Lauren M.; Nielsen, Torben N.; Arkin, Adam P.
- PLOS Computational Biology, Vol. 17, Issue 5
Accelerated Profile HMM Searches
journal, October 2011
- Eddy, Sean R.
- PLoS Computational Biology, Vol. 7, Issue 10
metaFlye: scalable long-read metagenome assembly using repeat graphs
journal, October 2020
- Kolmogorov, Mikhail; Bickhart, Derek M.; Behsaz, Bahar
- Nature Methods, Vol. 17, Issue 11
Binning metagenomic contigs by coverage and composition
journal, September 2014
- Alneberg, Johannes; Bjarnason, Brynjar Smári; de Bruijn, Ino
- Nature Methods, Vol. 11, Issue 11
The carbohydrate-active enzymes database (CAZy) in 2013
journal, November 2013
- Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie
- Nucleic Acids Research, Vol. 42, Issue D1
MetaPhlAn2 for enhanced metagenomic taxonomic profiling
journal, September 2015
- Truong, Duy Tin; Franzosa, Eric A.; Tickle, Timothy L.
- Nature Methods, Vol. 12, Issue 10
GUNC: detection of chimerism and contamination in prokaryotic genomes
journal, June 2021
- Orakov, Askarbek; Fullam, Anthony; Coelho, Luis Pedro
- Genome Biology, Vol. 22, Issue 1
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation
journal, March 2017
- Koren, Sergey; Walenz, Brian P.; Berlin, Konstantin
- Genome Research, Vol. 27, Issue 5
Microbial abundance, activity and population genomic profiling with mOTUs2
journal, March 2019
- Milanese, Alessio; Mende, Daniel R.; Paoli, Lucas
- Nature Communications, Vol. 10, Issue 1
Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen
journal, February 2018
- Stewart, Robert D.; Auffret, Marc D.; Warr, Amanda
- Nature Communications, Vol. 9, Issue 1
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
journal, October 2009
- Schloss, P. D.; Westcott, S. L.; Ryabin, T.
- Applied and Environmental Microbiology, Vol. 75, Issue 23, p. 7537-7541
A new view of the tree of life
journal, April 2016
- Hug, Laura A.; Baker, Brett J.; Anantharaman, Karthik
- Nature Microbiology, Vol. 1, Issue 5
BLAST+: architecture and applications
journal, January 2009
- Camacho, Christiam; Coulouris, George; Avagyan, Vahram
- BMC Bioinformatics, Vol. 10, Issue 1
Biases in genome reconstruction from metagenomic data
journal, January 2020
- Nelson, William C.; Tully, Benjamin J.; Mobberley, Jennifer M.
- PeerJ, Vol. 8
Community structure and metabolism through reconstruction of microbial genomes from the environment
journal, February 2004
- Tyson, Gene W.; Chapman, Jarrod; Hugenholtz, Philip
- Nature, Vol. 428, Issue 6978
RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes
journal, February 2015
- Brettin, Thomas; Davis, James J.; Disz, Terry
- Scientific Reports, Vol. 5, Issue 1
QIIME allows analysis of high-throughput community sequencing data
journal, April 2010
- Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse
- Nature Methods, Vol. 7, Issue 5
dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication
journal, July 2017
- Olm, Matthew R.; Brown, Christopher T.; Brooks, Brandon
- The ISME Journal, Vol. 11, Issue 12
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
journal, November 2018
- Jain, Chirag; Rodriguez-R, Luis M.; Phillippy, Adam M.
- Nature Communications, Vol. 9, Issue 1
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
journal, August 2019
- Kim, Daehwan; Paggi, Joseph M.; Park, Chanhee
- Nature Biotechnology, Vol. 37, Issue 8
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
journal, September 2017
- Parks, Donovan H.; Rinke, Christian; Chuvochina, Maria
- Nature Microbiology, Vol. 2, Issue 11
A genomic catalog of Earth’s microbiomes
journal, November 2020
- Nayfach, Stephen; Roux, Simon; Seshadri, Rekha
- Nature Biotechnology, Vol. 39, Issue 4, p. 499-509
Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data
journal, January 2020
- Chong, Jasmine; Liu, Peng; Zhou, Guangyan
- Nature Protocols, Vol. 15, Issue 3
Bringing your tools to CyVerse Discovery Environment using Docker
journal, January 2016
- Devisetty, Upendra Kumar; Kennedy, Kathleen; Sarando, Paul
- F1000Research, Vol. 5
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
journal, February 2015
- Pertea, Mihaela; Pertea, Geo M.; Antonescu, Corina M.
- Nature Biotechnology, Vol. 33, Issue 3
Complex archaea that bridge the gap between prokaryotes and eukaryotes
journal, May 2015
- Spang, Anja; Saw, Jimmy H.; Jørgensen, Steffen L.
- Nature, Vol. 521, Issue 7551
Recovering prokaryotic genomes from host-associated, short-read shotgun metagenomic sequencing data
journal, April 2021
- Saheb Kashaf, Sara; Almeida, Alexandre; Segre, Julia A.
- Nature Protocols, Vol. 16, Issue 5
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes
journal, October 2018
- Chen, I-Min A.; Chu, Ken; Palaniappan, Krishna
- Nucleic Acids Research, Vol. 47, Issue D1
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
journal, October 2010
- Matsen, Frederick A.; Kodner, Robin B.; Armbrust, E. Virginia
- BMC Bioinformatics, Vol. 11, Issue 1
Community-led, integrated, reproducible multi-omics with anvi’o
journal, December 2020
- Eren, A. Murat; Kiefl, Evan; Shaiber, Alon
- Nature Microbiology, Vol. 6, Issue 1
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
journal, November 2013
- Overbeek, Ross; Olson, Robert; Pusch, Gordon D.
- Nucleic Acids Research, Vol. 42, Issue D1
A standardized archaeal taxonomy for the Genome Taxonomy Database
journal, June 2021
- Rinke, Christian; Chuvochina, Maria; Mussig, Aaron J.
- Nature Microbiology, Vol. 6, Issue 7
MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004
- Edgar, R. C.
- Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
journal, October 2016
- Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A.
- Nature Communications, Vol. 7, Issue 1
The genome portal of the Department of Energy Joint Genome Institute: 2014 updates
journal, November 2013
- Nordberg, Henrik; Cantor, Michael; Dusheyko, Serge
- Nucleic Acids Research, Vol. 42, Issue D1
MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies
journal, January 2019
- Kang, Dongwan D.; Li, Feng; Kirton, Edward
- PeerJ, Vol. 7
The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans
journal, January 2018
- Tully, Benjamin J.; Graham, Elaina D.; Heidelberg, John F.
- Scientific Data, Vol. 5, Issue 1
Ionic Liquids Impact the Bioenergy Feedstock-Degrading Microbiome and Transcription of Enzymes Relevant to Polysaccharide Hydrolysis
journal, December 2016
- Wu, Yu-Wei; Higgins, Brendan; Yu, Chaowei
- mSystems, Vol. 1, Issue 6
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014
- Love, Michael I.; Huber, Wolfgang; Anders, Simon
- Genome Biology, Vol. 15, Issue 12
Genome Extraction from Shotgun Metagenome Sequence Data
dataset, January 2021
- Chivian, Dylan; Jungbluth, Sean; Dehal, Paramvir
- U.S. Department of Energy Systems Biology Knowledgebase