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GENOME REPORT: High-quality genome assemblies of 15 Drosophila species generated using Nanopore sequencing

https://doi.org/10.1101/267393
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1038/hdy.2008.49openalex-snapshot
Genome size diversity in the family Drosophilidae
inferredcites →https://doi.org/10.1038/nature06341openalex-snapshot
Evolution of genes and genomes on the Drosophila phylogeny
inferredcites →https://doi.org/10.1038/nature22971openalex-snapshot
Improved maize reference genome with single-molecule technologies
inferredcites →https://doi.org/10.1038/nbt.3238openalex-snapshot
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
inferredcites →https://doi.org/10.1038/nbt.4060openalex-snapshot
Nanopore sequencing and assembly of a human genome with ultra-long reads
inferredcites →https://doi.org/10.1038/nmeth.4184openalex-snapshot
Detecting DNA cytosine methylation using nanopore sequencing
inferredcites →https://doi.org/10.1038/nrg3933openalex-snapshot
Genetic variation and the de novo assembly of human genomes
inferredcites →https://doi.org/10.1038/s41467-018-03016-2openalex-snapshot
High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell
inferredcites →https://doi.org/10.1038/s41598-016-0001-8openalex-snapshot
Ultrastructural Characterization of the Lower Motor System in a Mouse Model of Krabbe Disease
inferredcites →https://doi.org/10.1038/sdata.2014.45openalex-snapshot
Long-read, whole-genome shotgun sequence data for five model organisms
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btv351openalex-snapshot
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
inferredcites →https://doi.org/10.1093/bioinformatics/btw152openalex-snapshot
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot
Minimap2: pairwise alignment for nucleotide sequences
inferredcites →https://doi.org/10.1093/femsyr/fox074openalex-snapshot
Nanopore sequencing enables near-complete de novo assembly of Saccharomyces cerevisiae reference strain CEN.PK113-7D
inferredcites →https://doi.org/10.1093/gbe/evt034openalex-snapshot
Linking Genomics and Ecology to Investigate the Complex Evolution of an Invasive Drosophila Pest
inferredcites →https://doi.org/10.1093/molbev/msg236openalex-snapshot
Temporal Patterns of Fruit Fly (Drosophila) Evolution Revealed by Mutation Clocks
inferredcites →https://doi.org/10.1093/molbev/mss150openalex-snapshot
Estimating Divergence Dates and Substitution Rates in the Drosophila Phylogeny
inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1093/nar/27.11.2369openalex-snapshot
Alignment of whole genomes
inferredcites →https://doi.org/10.1101/gr.139873.112openalex-snapshot
Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana
inferredcites →https://doi.org/10.1101/gr.185579.114openalex-snapshot
The Release 6 reference sequence of the Drosophila melanogaster genome
inferredcites →https://doi.org/10.1101/gr.214270.116openalex-snapshot
Fast and accurate de novo genome assembly from long uncorrected reads
inferredcites →https://doi.org/10.1101/gr.215087.116openalex-snapshot
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation
inferredcites →https://doi.org/10.1101/gr.221184.117openalex-snapshot
MinION-based long-read sequencing and assembly extends the Caenorhabditis elegans reference genome
inferredcites →https://doi.org/10.1126/science.287.5461.2185openalex-snapshot
The Genome Sequence of Drosophila melanogaster
inferredcites →https://doi.org/10.1371/journal.pone.0112963openalex-snapshot
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
inferredcites →https://doi.org/10.1371/journal.pone.0173505openalex-snapshot
The mode and tempo of genome size evolution in the subgenus Sophophora
inferredcites →https://doi.org/10.1534/g3.113.008185openalex-snapshot
Genome of Drosophila suzukii, the Spotted Wing Drosophila
inferredcites →https://doi.org/10.1534/g3.116.037598openalex-snapshot
Single-Molecule Sequencing of the Drosophila serrata Genome
inferredcites →https://doi.org/10.1534/g3.116.038885openalex-snapshot
Genetic and Transgenic Reagents for Drosophila simulans , D. mauritiana , D. yakuba , D. santomea , and D. virilis
inferredcites →https://doi.org/10.1534/genetics.107.075069openalex-snapshot
Analysis of Drosophila Species Genome Size and Satellite DNA Content Reveals Significant Differences Among Strains as Well as Between Species
inferredcites →https://doi.org/10.1534/genetics.113.152710openalex-snapshot
Genome Engineering of Drosophila with the CRISPR RNA-Guided Cas9 Nuclease
inferredcites →https://doi.org/10.1534/genetics.115.180208openalex-snapshot
The Transgenic RNAi Project at Harvard Medical School: Resources and Validation
inferredcites →https://doi.org/10.1534/genetics.117.300583openalex-snapshot
Phylogeny of the Genus Drosophila
inferredcites →https://doi.org/10.1554/0014-3820(2002)056[2262:goadip]2.0.co;2openalex-snapshot
GENETICS OF A DIFFERENCE IN PIGMENTATION BETWEEN DROSOPHILA YAKUBA AND DROSOPHILA SANTOMEA

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/978-3-319-97280-0_7openalex-snapshot
Genome Sequence of Castor Bean
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty1045openalex-snapshot
poreTally: run and publish de novo nanopore assembler benchmarks
inferred← citeshttps://doi.org/10.1101/425710openalex-snapshot
Long-read based assembly and annotation of a Drosophila simulans genome
inferred← citeshttps://doi.org/10.1101/434118openalex-snapshot
Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome
inferred← citeshttps://doi.org/10.1101/434670openalex-snapshot
Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies
inferred← citeshttps://doi.org/10.1101/gr.263442.120openalex-snapshot
Evolution of genome structure in the Drosophila simulans species complex
inferred← citeshttps://doi.org/10.1186/s12915-019-0728-3openalex-snapshot
Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies
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