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A computational genomics pipeline for prokaryotic sequencing projects

Andrey O. Kislyuk, Lee S. Katz, Sonia Agrawal, Matthew S. Hagen, Andrew B. Conley, Pushkala Jayaraman, Viswateja Nelakuditi, Jay C. Humphrey, Scott A. Sammons, Dhwani Govil, Raydel D. Mair, Kathleen M. Tatti (+4 others)
2010 Computer applications in the biosciences : CABIOS  
Results: We present a self-contained, automated high-throughput open source genome sequencing and computational genomics pipeline suitable for prokaryotic sequencing projects.  ...  Because every component of the pipeline is executed on a local machine with no need to access resources over the Internet, the pipeline is suitable for projects of a sensitive nature.  ...  ACKNOWLEDGEMENTS We are grateful to all participants of the Georgia Tech Computational Genomics class; to Leonardo Mariño-Ramírez for valuable guidance and input; and to Joshua S.  ... 
doi:10.1093/bioinformatics/btq284 pmid:20519285 pmcid:PMC2905547 fatcat:6tkhera5jrgehmn7fgk76lekfe

RAMPART: a workflow management system for de novo genome assembly

Daniel Mapleson, Nizar Drou, David Swarbreck
2015 Computer applications in the biosciences : CABIOS  
results for their particular genome and sequenced reads.  ...  Motivation: The de novo assembly of genomes from whole-genome shotgun sequence data is a computationally intensive, multi-stage task and it is not known a priori which methods and parameter settings will  ...  Thanks also to all RAMPART users and the manuscript reviewers for their valuable feedback.  ... 
doi:10.1093/bioinformatics/btv056 pmid:25637556 pmcid:PMC4443680 fatcat:xtstsaynqnafdbe3vkeziubgme

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Nuala A. O'Leary, Mathew W. Wright, J. Rodney Brister, Stacy Ciufo, Diana Haddad, Rich McVeigh, Bhanu Rajput, Barbara Robbertse, Brian Smith-White, Danso Ako-Adjei, Alexander Astashyn, Azat Badretdin (+43 others)
2015 Nucleic Acids Research  
The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http:/  ...  We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes  ...  and accuracy of the represented sequence, structural annotation, and functional annotation.  ... 
doi:10.1093/nar/gkv1189 pmid:26553804 pmcid:PMC4702849 fatcat:2bm7d5coyvfotaj23hnj3mce6m

Update on RefSeq microbial genomes resources

Tatiana Tatusova, Stacy Ciufo, Scott Federhen, Boris Fedorov, Richard McVeigh, Kathleen O'Neill, Igor Tolstoy, Leonid Zaslavsky
2014 Nucleic Acids Research  
A number of improvements have been incorporated into the Prokaryotic Genome Annotation Pipeline.  ...  Prokaryotic genome sequences are the most rapidly growing part of the collection.  ...  The NCBI Prokaryotic Genome Annotation pipeline is offered as a service to GenBank submitters and is used for consistent annotation of RefSeq genomes.  ... 
doi:10.1093/nar/gku1062 pmid:25510495 pmcid:PMC4383903 fatcat:52oqwfkoircovp4jgymgm4nhry

ZGA: a flexible pipeline for read processing, de novo assembly and annotation of prokaryotic genomes [article]

A.A. Korzhenkov
2021 bioRxiv   pre-print
To solve this problem, a bioinformatic pipeline was developed to conduct a user from raw sequencing reads to annotated bacterial or archaeal genome ready for deposition to any INSDC database as NCBI, ENA  ...  Despite increasing availability of genome sequencing by itself, genome assembly and annotation could be a challenge for an inexperienced researcher.  ...  Funding This work has been supported by the Ministry of Science and Higher Education of Russian Federation allocated to the Kurchatov Center for Genome Research (grant No 075-15-2019-1659.  ... 
doi:10.1101/2021.04.27.441618 fatcat:utmln6wi5fcxnmitt5lsha4kb4

gcType: a high-quality type strain genome database for microbial phylogenetic and functional research

Wenyu Shi, Qinglan Sun, Guomei Fan, Sugawara Hideaki, Ohkuma Moriya, Takashi Itoh, Yuguang Zhou, Man Cai, Song-Gun Kim, Jung-Sook Lee, Ivo Sedlacek, David R Arahal (+24 others)
2020 Nucleic Acids Research  
In this study, we describe web-based data analysis pipelines for genomic analyses and genome-based taxonomy, which could serve as a one-stop platform for the identification of prokaryotic species.  ...  As the depository of the Global Catalogue of Microorganisms (GCM) 10K prokaryotic type strain sequencing project, Global Catalogue of Type Strain (gcType) has published 1049 type strain genomes sequenced  ...  ACKNOWLEDGEMENTS We would like to thank the members of the World Federation for Culture Collections for the GCM 10K sequencing project.  ... 
doi:10.1093/nar/gkaa957 pmid:33119759 fatcat:7sn5nvlxgrhx5aw53k6emsyt2u

Ergatis: a web interface and scalable software system for bioinformatics workflows

J. Orvis, J. Crabtree, K. Galens, A. Gussman, J. M. Inman, E. Lee, S. Nampally, D. Riley, J. P. Sundaram, V. Felix, B. Whitty, A. Mahurkar (+3 others)
2010 Bioinformatics  
Ergatis contains preconfigured components and template pipelines for a number of common bioinformatics tasks such as prokaryotic genome annotation and genome comparisons.  ...  Ergatis supports highthroughput batch processing on distributed compute clusters and has been used for data management in a number of genome annotation and comparative genomics projects.  ...  ACKNOWLEDGEMENTS We would like to thank both the developers on the project and the user community who continue to suggest new features and improve the project.  ... 
doi:10.1093/bioinformatics/btq167 pmid:20413634 pmcid:PMC2881353 fatcat:y3q4bmjwzbddhhsqshjajxuuyi

InteractomeSeq: a web server for the identification and profiling of domains and epitopes from phage display and next generation sequencing data

Simone Puccio, Giorgio Grillo, Arianna Consiglio, Maria Felicia Soluri, Daniele Sblattero, Diego Cotella, Claudio Santoro, Sabino Liuni, Gianluca De Bellis, Enrico Lugli, Clelia Peano, Flavio Licciulli
2020 Nucleic Acids Research  
InteractomeSeq is a web server allowing data analysis of protein domains ('domainome') or epitopes ('epitome') from either Eukaryotic or Prokaryotic genomic phage libraries generated and selected by following  ...  However, from a bioinformatics point of view, the analysis of this kind of data was always performed by adapting tools designed for other purposes, thus not considering the noise background typical of  ...  and administrative support, Nicola Losito (Institute of Biomedical Technologies, National Research Council, Bari) for server management support.  ... 
doi:10.1093/nar/gkaa363 pmid:32402076 fatcat:7tw7m42rb5eizhabdcvjg3r7py

Large-scale quality assessment of prokaryotic genomes with metashot/prok-quality

Davide Albanese, Claudio Donati
2021 F1000Research  
A comprehensive, automated and easy-to-use computational workflow for the quality assessment of draft prokaryotic genomes, based on container technology, would greatly improve reproducibility and reusability  ...  We present metashot/prok-quality, a container-enabled Nextflow pipeline for quality assessment and genome dereplication.  ...  Acknowledgements The authors wish to thank Giuseppe Cossu and the Information Technology team of the Fondazione Edmund Mach for technical support.  ... 
doi:10.12688/f1000research.54418.1 pmid:35136576 pmcid:PMC8804904 fatcat:dzwzkpna3neuvew4w6csnuzaoy

CharProtDB: a database of experimentally characterized protein annotations

R. Madupu, A. Richter, R. J. Dodson, L. Brinkac, D. Harkins, S. Durkin, S. Shrivastava, G. Sutton, D. Haft
2011 Nucleic Acids Research  
Craig Venter Institute (JCVI) [formerly The Institute of Genomic Research (TIGR)] as part of their prokaryotic genome sequencing projects.  ...  It provides a source of direct rather than transitive assignments of function, designed to support automated annotation pipelines.  ...  ACKNOWLEDGEMENTS The authors would like to thank past and present colleagues at the JCVI Bioinformatics and Information Technology departments for scientific contributions and technical support including  ... 
doi:10.1093/nar/gkr1133 pmid:22140108 pmcid:PMC3245046 fatcat:bt5qedijejatvoffq7dq7q4f5y

Meeting report: a workshop on Best Practices in Genome Annotation

R. Madupu, L. M. Brinkac, J. Harrow, L. G. Wilming, U. Bohme, P. Lamesch, L. I. Hannick
2010 Database: The Journal of Biological Databases and Curation  
These requirements depend on whether the project is part of a comparative genome-sequencing project or a genome project for an organism for which there is no sequence data available from a closely related  ...  Artemis is a free, easy to use sequence viewer and annotation tool for prokaryotic and eukaryotic genomes.  ... 
doi:10.1093/database/baq001 pmid:20428316 pmcid:PMC2860899 fatcat:ibdlwzv74veqrb6mzl7nkyr3km

RefSeq microbial genomes database: new representation and annotation strategy

Tatiana Tatusova, Stacy Ciufo, Boris Fedorov, Kathleen O'Neill, Igor Tolstoy
2013 Nucleic Acids Research  
Microbial genomes can now be sequenced in a matter of hours, which has led to a significant increase in the number of assembled genomes deposited in the public archives.  ...  New strategies have been developed for the annotation and representation of reference genomes and sequence variations derived from population studies and clinical outbreaks.  ...  Reannotation project Historically, RefSeq prokaryotic genomes relied on author-submitted annotation.  ... 
doi:10.1093/nar/gkt1274 pmid:24316578 pmcid:PMC3965038 fatcat:7yynuxostnhpjlx6mcrezaekqq

RefSeq microbial genomes database: new representation and annotation strategy

T. Tatusova, S. Ciufo, B. Fedorov, K. O'Neill, I. Tolstoy
2015 Nucleic Acids Research  
Microbial genomes can now be sequenced in a matter of hours, which has led to a significant increase in the number of assembled genomes deposited in the public archives.  ...  New strategies have been developed for the annotation and representation of reference genomes and sequence variations derived from population studies and clinical outbreaks.  ...  Reannotation project Historically, RefSeq prokaryotic genomes relied on author-submitted annotation.  ... 
doi:10.1093/nar/gkv278 pmid:25824943 pmcid:PMC4402550 fatcat:o3opkwpazfdvrkml2uliuxy2py

Draft Genome Sequences of Five Enterococcus Species Isolated from the Gut of Patients with Suspected Clostridium difficile Infection

Eduardo Castro-Nallar, Sandro L. Valenzuela, Sebastián Baquedano, Carolina Sánchez, Fabiola Fernández, Annette N. Trombert
2017 Genome Announcements  
We present draft genome sequences of five Enterococcus species from patients suspected of Clostridium difficile infection. Genome completeness was confirmed by presence of bacterial orthologs (97%).  ...  We annotated the assembled genome sequences using the NCBI Prokaryotic Genome Annotation Pipeline (released 2013) (10) .  ...  -N. thanks the high-performance computing facility of George Washington University, ColonialOne, for providing data storage, support, and computing power for genomic analyses (colonialone.gwu.edu).  ... 
doi:10.1128/genomea.00379-17 pmid:28522725 pmcid:PMC5477334 fatcat:fm2ab2pq3ngsjdf7szwm3tbojm

GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes

Jia Zhang, Ming-kun Yang, Honghui Zeng, Feng Ge
2016 Molecular & Cellular Proteomics  
This software is a powerful tool for genome annotation and global discovery of PTMs and is applicable to any sequenced prokaryotic organism; we expect that it will become an integral part of ongoing genome  ...  Although the number of sequenced prokaryotic genomes is growing rapidly, experimentally verified annotation of prokaryotic genome remains patchy and challenging.  ...  Thousands of prokaryotic genomes have been sequenced with the rapid advance of massively parallel sequencing technologies.  ... 
doi:10.1074/mcp.m116.060046 pmid:27630248 pmcid:PMC5098048 fatcat:rjvarp6vyrbtdiyilihoyb5oza
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