KBase Narrative - Mse_Genome_Assembly

Name: KBase Narrative - Mse_Genome_Assembly
Published: Wed Sep 14 00:00:00 EDT 2022

Rastegar, Kiarash

doi:10.25982/116829.47/1887425

KBase Narrative - Mse_Genome_Assembly

Dataset · Wed Sep 14 00:00:00 EDT 2022

DOI:https://doi.org/10.25982/116829.47/1887425· OSTI ID:1887425

Rastegar, Kiarash ^[1]

San Diego State University; Lawrence Berkeley National Laboratory (LBNL)

Upon investigating the gut microbiome of mice for microbes related to Polycystic Ovary Syndrome (PCOS), our team found 2 metagenomes that could not be classified using alignment based methods. To further investigate microbial species from these samples, we used common MAGs workflow to create draft genomes which were then later taxonomically classified using GTDB-tk app.

View Dataset

Research Organization:: U.S. Department of Energy Systems Biology Knowledgebase

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI ID:: 1887425

Country of Publication:: United States

Language:: English

References (24)

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database Chaumeil, Pierre-Alain; Mussig, Aaron J.; Hugenholtz, Philip Bioinformatics https://doi.org/10.1093/bioinformatics/btz848	journal	November 2019
KBase: The United States Department of Energy Systems Biology Knowledgebase Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S. Nature Biotechnology, Vol. 36, Issue 7 https://doi.org/10.1038/nbt.4163	journal	July 2018
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A. Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402 https://doi.org/10.1093/nar/25.17.3389	journal	September 1997
Identifying bacterial genes and endosymbiont DNA with Glimmer Delcher, Arthur L.; Bratke, Kirsten A.; Powers, Edwin C. Bioinformatics, Vol. 23, Issue 6 https://doi.org/10.1093/bioinformatics/btm009	journal	January 2007
The RAST Server: Rapid Annotations using Subsystems Technology Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A. BMC Genomics, Vol. 9, Issue 1, Article No. 75 https://doi.org/10.1186/1471-2164-9-75	journal	January 2008
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets Wu, Yu-Wei; Simmons, Blake A.; Singer, Steven W. Bioinformatics, Vol. 32, Issue 4 https://doi.org/10.1093/bioinformatics/btv638	journal	October 2015
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy Sieber, Christian M. K.; Probst, Alexander J.; Sharrar, Allison Nature Microbiology, Vol. 3, Issue 7 https://doi.org/10.1038/s41564-018-0171-1	journal	May 2018
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm Wu, Yu-Wei; Tang, Yung-Hsu; Tringe, Susannah G. Microbiome, Vol. 2, Issue 1 https://doi.org/10.1186/2049-2618-2-26	journal	August 2014
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) Overbeek, Ross; Olson, Robert; Pusch, Gordon D. Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1226	journal	November 2013
BLAST+: architecture and applications Camacho, Christiam; Coulouris, George; Avagyan, Vahram BMC Bioinformatics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2105-10-421	journal	January 2009
Identification, variation and transcription of pneumococcal repeat sequences Croucher, Nicholas J.; Vernikos, Georgios S.; Parkhill, Julian BMC Genomics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2164-12-120	journal	February 2011
DRAM for distilling microbial metabolism to automate the curation of microbiome function Shaffer, Michael; Borton, Mikayla A.; McGivern, Bridget B. Nucleic Acids Research, Vol. 48, Issue 16 https://doi.org/10.1093/nar/gkaa621	journal	August 2020
PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies Akhter, Sajia; Aziz, Ramy K.; Edwards, Robert A. Nucleic Acids Research, Vol. 40, Issue 16 https://doi.org/10.1093/nar/gks406	journal	May 2012
BLAT---The BLAST-Like Alignment Tool Kent, W. J. Genome Research, Vol. 12, Issue 4 https://doi.org/10.1101/gr.229202	journal	March 2002
Circular genome visualization and exploration using CGView Stothard, P.; Wishart, D. S. Bioinformatics, Vol. 21, Issue 4 https://doi.org/10.1093/bioinformatics/bti054	journal	October 2004
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes Brettin, Thomas; Davis, James J.; Disz, Terry Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep08365	journal	February 2015
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P. PLoS ONE, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pone.0009490	journal	March 2010
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T. Genome Research, Vol. 25, Issue 7 https://doi.org/10.1101/gr.186072.114	journal	May 2015
Fast and sensitive protein alignment using DIAMOND Buchfink, Benjamin; Xie, Chao; Huson, Daniel H. Nature Methods, Vol. 12, Issue 1 https://doi.org/10.1038/nmeth.3176	journal	November 2014
Translational recoding in archaea Cobucci-Ponzano, Beatrice; Rossi, Mosè; Moracci, Marco Extremophiles, Vol. 16, Issue 6 https://doi.org/10.1007/s00792-012-0482-8	journal	September 2012
FIGfams: yet another set of protein families Meyer, Folker; Overbeek, Ross; Rodriguez, Alex Nucleic Acids Research, Vol. 37, Issue 20 https://doi.org/10.1093/nar/gkp698	journal	September 2009
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life Parks, Donovan H.; Chuvochina, Maria; Waite, David W. Nature Biotechnology, Vol. 36, Issue 10 https://doi.org/10.1038/nbt.4229	journal	August 2018
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree Matsen, Frederick A.; Kodner, Robin B.; Armbrust, E. Virginia BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-538	journal	October 2010

Similar Records

KBase Narrative - Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed site

Dataset · Thu Oct 26 00:00:00 EDT 2023 · OSTI ID:2203552

A Genomic Catalogue of Earth’s Microbiomes - Introductory KBase Narrative

Dataset · Tue Dec 31 23:00:00 EST 2019 · OSTI ID:1670777

Dataset for the Danczak et al., 2025 manuscript about bacterial-fungal interactions

Dataset · Wed Aug 06 00:00:00 EDT 2025 · OSTI ID:2574929

KBase Narrative - Mse_Genome_Assembly

Citation Formats

References (24)

Similar Records

Related Subjects