Rat Genome Assemblies, Annotation, and Variant Repository.
Sign Up to like & getrecommendations! Published in 2019 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-9581-3_2
Abstract: The first and only published version of the rat reference genome sequence was RGSC3.1, accomplished by the Rat Genome Sequencing Project Consortium. Here we present the history of the community effort in the correction of… read more here.
Keywords: assemblies annotation; linkage; rat genome; rat ... See more keywords
excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btad198
Abstract: Summary Exclusion regions are sections of reference genomes with abnormal pileups of short sequencing reads. Removing reads overlapping them improves biological signal, and these benefits are most pronounced in differential analysis settings. Several labs created… read more here.
Keywords: exclusion; exclusion sets; grcm39; genome assemblies ... See more keywords
Chromosome-Level Genome Assemblies of Two Hypnales (Mosses) Reveal High Intergeneric Synteny
Sign Up to like & getrecommendations! Published in 2022 at "Genome Biology and Evolution"
DOI: 10.1093/gbe/evac020
Abstract: Abstract Mosses compose one of the three lineages of bryophytes. Today, about 13,000 species of mosses are recognized from across the globe, and at least one-third of this diversity composes the Hypnales, a lineage characterized… read more here.
Keywords: genome assemblies; curvifolium; chromosome level; level genome ... See more keywords
Highly Contiguous Genome Assemblies of the Guinea Paper Wasp (Polistes exclamans) and Mischocyttarus mexicanus
Sign Up to like & getrecommendations! Published in 2022 at "Genome Biology and Evolution"
DOI: 10.1093/gbe/evac110
Abstract: Abstract Paper wasps are a model system for the study of social evolution due to a high degree of inter- and intraspecific variation in cooperation, aggression, and visual signals of social status. Increasing the taxonomic… read more here.
Keywords: polistes exclamans; genome assemblies; mexicanus; genome ... See more keywords
polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies
Sign Up to like & getrecommendations! Published in 2022 at "Genome Biology and Evolution"
DOI: 10.1093/gbe/evad020
Abstract: Long-read sequencing has revolutionized genome assembly, yielding highly contiguous, chromosome-level contigs. However, assemblies from some third generation long read technologies, such as Pacific Biosciences (PacBio) Continuous Long Reads (CLR), have a high error rate. Such… read more here.
Keywords: polishclr; nextflow workflow; clr; genome assemblies ... See more keywords
Tapping Culture Collections for Fungal Endophytes: First Genome Assemblies for Three Genera and Five Species in the Ascomycota
Sign Up to like & getrecommendations! Published in 2023 at "Genome Biology and Evolution"
DOI: 10.1093/gbe/evad038
Abstract: Abstract The Ascomycota form the largest phylum in the fungal kingdom and show a wide diversity of lifestyles, some involving associations with plants. Genomic data are available for many ascomycetes that are pathogenic to plants,… read more here.
Keywords: culture; fungal endophytes; culture collections; tapping culture ... See more keywords
The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkinsiana)
Sign Up to like & getrecommendations! Published in 2018 at "GigaScience"
DOI: 10.1093/gigascience/giy097
Abstract: Abstract Background Calamus simplicifolius and Daemonorops jenkinsiana are two representative rattans, the most significant material sources for the rattan industry. However, the lack of reference genome sequences is a major obstacle for basic and applied… read more here.
Keywords: simplicifolius daemonorops; daemonorops jenkinsiana; simplicifolius jenkinsiana; calamus simplicifolius ... See more keywords
Detection of plasmid contigs in draft genome assemblies using customized Kraken databases
Sign Up to like & getrecommendations! Published in 2021 at "Microbial Genomics"
DOI: 10.1099/mgen.0.000550
Abstract: Plasmids play an important role in bacterial evolution and mediate horizontal transfer of genes including virulence and antimicrobial resistance genes. Although short-read sequencing technologies have enabled large-scale bacterial genomics, the resulting draft genome assemblies are… read more here.
Keywords: kraken; contig; draft genome; plasmid ... See more keywords
Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants
Sign Up to like & getrecommendations! Published in 2019 at "Genome Research"
DOI: 10.1101/gr.251033.119
Abstract: Genome assemblies from diploid organisms create mosaic sequences alternating between parental alleles, which can create erroneous gene models and other problems. In animals, a popular strategy to generate haploid genome-resolved assemblies has been the sampling… read more here.
Keywords: cell sequencing; haploid; genome; pollen ... See more keywords
Hi‐C scaffolded short‐ and long‐read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution
Sign Up to like & getrecommendations! Published in 2021 at "Molecular Ecology Resources"
DOI: 10.1111/1755-0998.13443
Abstract: With the advent of chromatin‐interaction maps, chromosome‐level genome assemblies have become a reality for a wide range of organisms. Scaffolding quality is, however, difficult to judge. To explore this gap, we generated multiple chromosome‐scale genome… read more here.
Keywords: genome; chromosome; sea lion; genome assemblies ... See more keywords
Insights into mammalian TE diversity through the curation of 248 genome assemblies
Sign Up to like & getrecommendations! Published in 2023 at "Science"
DOI: 10.1126/science.abn1430
Abstract: We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content… read more here.
Keywords: curation; genome assemblies; dna transposons; diversity ... See more keywords