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Assembly: a resource for assembled genomes at NCBI
2015
Nucleic Acids Research
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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
2015
The Plant Genome
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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
2019
PLoS ONE
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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
2021
Microbiology Resource Announcements
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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]
2021
bioRxiv
pre-print
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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
2021
GigaScience
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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
2018
BMC Genomics
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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
2017
F1000Research
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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
2015
Genome Biology
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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
2019
Microbiology Resource Announcements
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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
2016
Frontiers in Microbiology
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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
2021
Microbiology Resource Announcements
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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
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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
2017
Genome Research
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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
2021
eLife
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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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