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Assembly: a resource for assembled genomes at NCBI

Paul A. Kitts, Deanna M. Church, Françoise Thibaud-Nissen, Jinna Choi, Vichet Hem, Victor Sapojnikov, Robert G. Smith, Tatiana Tatusova, Charlie Xiang, Andrey Zherikov, Michael DiCuccio, Terence D. Murphy (+2 others)
2015 Nucleic Acids Research  
Links in the Assembly Resource allow users to easily download sequence and annotations for current versions of genome assemblies from the NCBI genomes FTP site.  ...  The NCBI Assembly database (www.ncbi.nlm.nih. gov/assembly/) provides stable accessioning and data tracking for genome assembly data.  ...  ACKNOWLEDGEMENTS We thank all of our colleagues who provided suggestions and feedback on the Assembly resource and genomes FTP redesign, in particular: Mark Cavanaugh, Karen Clark, Bill Klimke, Ilene Mizrachi  ... 
doi:10.1093/nar/gkv1226 pmid:26578580 pmcid:PMC4702866 fatcat:2snbt2r7jjdczkqiyjihn5jpxi

Optimizing Transcriptome Assemblies for Leaf and Seedling by Combining Multiple Assemblies from Three De Novo Assemblers

Shu Chen, J. Scott McElroy, Fenny Dane, Eric Peatman
2015 The Plant Genome  
A crucial first step for a successful transcriptomics-based study is the building of a high-quality assembly.  ...  Due to rapid advances in sequencing technology, increasing amounts of genomic and transcriptomic data are available for plant species, presenting enormous challenges for biocomputing analysis.  ...  The RNA-seq data for goosegrass leaf were submitted to the NCBI SRA database (accession no.: SRR1560465) and the Main and Alternate assemblies to the TSA database (accession no.: SUB661580) under the BioProject  ... 
doi:10.3835/plantgenome2014.10.0064 pmid:33228277 fatcat:ty3fuwskb5aovnokcg766tsl6e

Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies

Giltae Song, Jongin Lee, Juyeon Kim, Seokwoo Kang, Hoyong Lee, Daehong Kwon, Daehwan Lee, Gregory I. Lang, J. Michael Cherry, Jaebum Kim, Maureen J. Donlin
2019 PLoS ONE  
For this type of study, a chromosome-level sequence assembly of the strain or population at time zero is required to compare with the genomes derived later.  ...  Genomic data have become major resources to understand complex mechanisms at fine-scale temporal and spatial resolution in functional and evolutionary genetic studies, including human diseases, such as  ...  For the outgroup in RACA, we used the genome sequence of Naumovozyma dairenensis (NCBI RefSeq: GCF_000227115.2).  ... 
doi:10.1371/journal.pone.0221858 pmid:31454399 pmcid:PMC6711525 fatcat:2psnxpb5bvb7jhxued5b5wk7qy

Assembly of Bacterial Genome Sequences from Metagenomes of Spacecraft Assembly Cleanrooms

Velislava Ilieva, Bruce Steel, Jennifer Pratscher, Karen Olsson-Francis, Michael C Macey
2021 Microbiology Resource Announcements  
Characterizing the microbiome of spacecraft assembly cleanrooms is important for planetary protection.  ...  We report two bacterial metagenome-assembled genomes (MAGs) reconstructed from metagenomes produced from cleanroom samples from the Kennedy Space Center's Payload Hazardous Servicing Facility (KSC-PHSF  ...  Contigs were binned into metagenome-assembled genomes (MAGs) using MaxBin v2.2.7 (8) .  ... 
doi:10.1128/mra.01439-20 pmid:33602737 fatcat:t2qy5wavy5cvxjw3wxkpin2fqq

Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes [article]

Romain Feron, Robert Michael Waterhouse
2021 bioRxiv   pre-print
Using this resource, we survey current taxonomic coverage and assembly quality at the NCBI, we examine how key assembly metrics relate to gene content completeness, and we compare results from using different  ...  Accurate and complete genome assemblies offer a comprehensive and reliable foundation upon which to advance our understanding of organismal biology at genetic, species, and ecosystem levels.  ...  Acknowledgments This research was supported by Novartis Foundation for medical-biological research grant #18B116 and Swiss National Science Foundation grants PP00P3_170664 and PP00P3_202669 to RMW.  ... 
doi:10.1101/2021.10.15.464561 fatcat:awtcfc57bvea7cjt4hbua646dm

De novo genome assemblies of butterflies

Emily A Ellis, Caroline G Storer, Akito Y Kawahara
2021 GigaScience  
Our assemblies will serve as a key resource for papilionid genomics, especially for researchers without computational resources.  ...  Here we examine quality trends in a taxonomically diverse and well-known group, butterflies (Papilionoidea), and provide draft, de novo assemblies for all available butterfly genomes.  ...  Acknowledgements The authors acknowledge the University of Florida Research Computing (https://www.rc.ufl.edu/) for providing computational resources and support that contributed to the research results  ... 
doi:10.1093/gigascience/giab041 pmid:34076242 pmcid:PMC8170690 fatcat:c2xnp2uhrzc6bjraghuymmsccq

Comparison of three assembly strategies for a heterozygous seedless grapevine genome assembly

Sagar Patel, Zhixiu Lu, Xiaozhu Jin, Padmapriya Swaminathan, Erliang Zeng, Anne Y. Fennell
2018 BMC Genomics  
In this study, three strategies were used to develop de novo Vitis vinifera 'Sultanina' genome assemblies for comparison with the inbred V. vinifera (PN40024 12X.v2) reference genome and a published Sultanina  ...  A PLAT*_GC pseudo-chromosome assembly with chromosome alignment to the reference genome V. vinifera, (PN40024 12X.v2) provides new information for use in seedless grape genetic mapping studies.  ...  Acknowledgements We acknowledge Brian Moore, Alan Carter and Fangping Mu for computational resource support.  ... 
doi:10.1186/s12864-018-4434-2 pmid:29343235 pmcid:PMC5773036 fatcat:iujzrd4iargwratkprbfuhq2ai

BlobTools: Interrogation of genome assemblies

Dominik R. Laetsch, Mark L. Blaxter
2017 F1000Research  
The goal of many genome sequencing projects is to provide a complete representation of a target genome (or genomes) as underpinning data for further analyses.  ...  We present BlobTools, a modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets.  ...  Acknowledgements We thank members of the Blaxter Nematode and Neglected Genomics lab in Edinburgh for support, criticism and suggestions.  ... 
doi:10.12688/f1000research.12232.1 fatcat:yhe2ibnwjjbv7edmanauy7npry

Extending reference assembly models

Deanna M Church, Valerie A Schneider, Karyn Steinberg, Michael C Schatz, Aaron R Quinlan, Chen-Shan Chin, Paul A Kitts, Bronwen Aken, Gabor T Marth, Michael M Hoffman, Javier Herrero, M Lisandra Mendoza (+2 others)
2015 Genome Biology  
The human genome reference assembly is crucial for aligning and analyzing sequence data, and for genome annotation, among other roles.  ...  However, the models and analysis assumptions that underlie the current assembly need revising to fully represent human sequence diversity.  ...  Acknowledgements We thank Daniel MacArthur, Jen Harrow and Mike Schatz, the organizers, for Genome Informatics 2014, for facilitating the GRC workshop, and Personalis Inc. for sponsorship.  ... 
doi:10.1186/s13059-015-0587-3 pmid:25651527 pmcid:PMC4305238 fatcat:252kfuuqpvbujibokrwuwznonu

Nuclear Genome Assembly of the Microalga Nannochloropsis salina CCMP1776

J. A. Ohan, B. T. Hovde, X. L. Zhang, K. W. Davenport, O. Chertkov, C. Han, S. N. Twary, S. R. Starkenburg, Antonis Rokas
2019 Microbiology Resource Announcements  
Here, we report an improved high-quality draft assembly and annotation for the nuclear genome of N. salina strain CCMP1776.  ...  Nannochloropsis salina is a halotolerant, high-lipid-producing microalga that is being explored as a biofuel production species.  ...  All sequences have been deposited in NCBI under BioSample number SAMN10354914 and GenBank accession number SDOX00000000. Genome assembly and annotations are also available at greenhouse.lanl.gov.  ... 
doi:10.1128/mra.00750-19 pmid:31672738 pmcid:PMC6953503 fatcat:uhpwyuashfdhfie7ht52i4h5aa

VirusTAP: Viral Genome-Targeted Assembly Pipeline

Akifumi Yamashita, Tsuyoshi Sekizuka, Makoto Kuroda
2016 Frontiers in Microbiology  
We have developed a web-based integrated NGS analysis tool for the viral genome (virus genome-targeted assembly pipeline: VirusTAP), which includes extensive sequence subtraction of host-or bacteria-related  ...  NGS reads prior to de novo assembly, leading to the prompt and accurate assembly of viral genome sequences from metagenomic NGS reads.  ...  Kei Haga for helpful suggestions.  ... 
doi:10.3389/fmicb.2016.00032 pmid:26870004 pmcid:PMC4735447 fatcat:eqont4syvvg5pmcdrzgauzlkzi

Metagenome Assembly and Metagenome-Assembled Genome Sequences from the Rhizosphere of Maize Plants in Mafikeng, South Africa

Olubukola O. Babalola, Rebaona R. Molefe, Adenike E. Amoo, Frank J. Stewart
2021 Microbiology Resource Announcements  
Metagenome-assembled genomes containing plant growth-promoting genes were reconstructed.  ...  The rhizosphere microbiome plays an essential role in enhancing the growth of plants, raising the need for comprehension of their metabolic abilities.  ...  The metagenome assemblies and the MAGs are available at the European Nucleotide Archive (ENA) under the project number PRJEB39783 with accession numbers SAMEA7159858 (F4R assembly), SAMEA7819642 (F4B assembly  ... 
doi:10.1128/mra.00954-20 pmid:33632860 fatcat:4akbrrp4iva5jkrx7vw4wdcbrm

Tripal EUtils: a Tripal module to increase exchange and reuse of genome assembly metadata

2019 Database: The Journal of Biological Databases and Curation  
Here, we describe our efforts to map metadata associated with genome assemblies between the National Center for Biotechnology Information (NCBI) data resources and the Chado biological database schema.  ...  We present mappings for multiple NCBI data structures and introduce a Tripal software module, Tripal EUtils, to pull metadata from NCBI into a Tripal/Chado database.  ...  Acknowledgements We thank Ethalinda Cannon, Gerard Lazo and three anonymous reviewers for the thoughtful reviews of this manuscript.  ... 
doi:10.1093/database/baz143 pmid:31960040 pmcid:PMC6989756 fatcat:5t63iw7xqfdgvcg3hya5ucti34

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

Valerie A. Schneider, Tina Graves-Lindsay, Kerstin Howe, Nathan Bouk, Hsiu-Chuan Chen, Paul A. Kitts, Terence D. Murphy, Kim D. Pruitt, Françoise Thibaud-Nissen, Derek Albracht, Robert S. Fulton, Milinn Kremitzki (+26 others)
2017 Genome Research  
and et al, ,"Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.  ...  A list of genome-wide and region-specific collaborators can be found at the GRC website (https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/ credits.shtml).  ...  The MGI would like to thank Susie Rock and Aye Wollam for their oversight of the assembly curation and finishing pipelines at the McDonnell Genome Institute.  ... 
doi:10.1101/gr.213611.116 pmid:28396521 pmcid:PMC5411779 fatcat:3hndzdxq3zgkphnvihuqqud4ry

Highly contiguous assemblies of 101 drosophilid genomes

Bernard Y Kim, Jeremy Wang, Danny E Miller, Olga Barmina, Emily Kay Delaney, Ammon Thompson, Aaron A Comeault, David Peede, Emmanuel R D'Agostino, Julianne Pelaez, Jessica M Aguilar, Diler Haji (+27 others)
2021 eLife  
These assemblies, along with a detailed laboratory protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology  ...  While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus.  ...  had insufficient Nanopore data for a Flye assembly. 658 For this line only and to consolidate all assemblies as a single resource, the same genome 659 assembly from Comeault et al. (2020) is both reported  ... 
doi:10.7554/elife.66405 pmid:34279216 pmcid:PMC8337076 fatcat:f2egoncekvfipoejsu4bd4rcmi
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