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Long-read based assembly and annotation of a Drosophila simulans genome

https://doi.org/10.1101/425710
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What this work says

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

inferredcites →https://doi.org/10.1002/ece3.2402openalex-snapshot
Ancestral population reconstitution from isofemale lines as a tool for experimental evolution
inferredcites →https://doi.org/10.1016/j.gpb.2015.08.002openalex-snapshot
PacBio Sequencing and its Applications
inferredcites →https://doi.org/10.1016/j.tig.2018.05.008openalex-snapshot
The Third Revolution in Sequencing Technology
inferredcites →https://doi.org/10.1016/j.ympev.2005.06.006openalex-snapshot
Historical biogeography of Drosophila simulans based on Y-chromosomal sequences
inferredcites →https://doi.org/10.1038/nature24286openalex-snapshot
DNA sequencing at 40: past, present and future
inferredcites →https://doi.org/10.1038/nbt.1621openalex-snapshot
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.2474openalex-snapshot
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
inferredcites →https://doi.org/10.1038/nmeth.2714openalex-snapshot
Assessment of transcript reconstruction methods for RNA-seq
inferredcites →https://doi.org/10.1038/nmeth.4035openalex-snapshot
Phased diploid genome assembly with single-molecule real-time sequencing
inferredcites →https://doi.org/10.1038/nprot.2013.084openalex-snapshot
De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity
inferredcites →https://doi.org/10.1038/nrg2958openalex-snapshot
Genome structural variation discovery and genotyping
inferredcites →https://doi.org/10.1038/s41588-017-0010-yopenalex-snapshot
Hidden genetic variation shapes the structure of functional elements in Drosophila
inferredcites →https://doi.org/10.1073/pnas.74.12.5463openalex-snapshot
DNA sequencing with chain-terminating inhibitors
inferredcites →https://doi.org/10.1089/cmb.2012.0021openalex-snapshot
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
inferredcites →https://doi.org/10.1093/bib/bbx147openalex-snapshot
Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btq057openalex-snapshot
Fast and SNP-tolerant detection of complex variants and splicing in short reads
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/molbev/mss150openalex-snapshot
Estimating Divergence Dates and Substitution Rates in the Drosophila Phylogeny
inferredcites →https://doi.org/10.1093/molbev/msx319openalex-snapshot
BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics
inferredcites →https://doi.org/10.1093/nar/30.11.2478openalex-snapshot
Fast algorithms for large-scale genome alignment and comparison
inferredcites →https://doi.org/10.1093/nar/gki458openalex-snapshot
AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints
inferredcites →https://doi.org/10.1093/nar/gkw1016openalex-snapshot
FlyBase at 25: looking to the future
inferredcites →https://doi.org/10.1093/nar/gkw654openalex-snapshot
Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage
inferredcites →https://doi.org/10.1101/267393openalex-snapshot
GENOME REPORT: High-quality genome assemblies of 15 Drosophila species generated using Nanopore sequencing
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.141689.112openalex-snapshot
A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence
inferredcites →https://doi.org/10.1101/gr.213405.116openalex-snapshot
Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii , a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm
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.6743907openalex-snapshot
MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes
inferredcites →https://doi.org/10.1111/1755-0998.12297openalex-snapshot
Genome assembly and annotation of a Drosophila simulans strain from Madagascar
inferredcites →https://doi.org/10.1111/1755-0998.12741openalex-snapshot
ReadTools: A universal toolkit for handling sequence data from different sequencing platforms
inferredcites →https://doi.org/10.1186/gb-2004-5-2-r12openalex-snapshot
Versatile and open software for comparing large genomes
inferredcites →https://doi.org/10.1371/journal.pbio.0050310openalex-snapshot
Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans
inferredcites →https://doi.org/10.1371/journal.pbio.2006348openalex-snapshot
De novo assembly of a young Drosophila Y chromosome using single-molecule sequencing and chromatin conformation capture
inferredcites →https://doi.org/10.1371/journal.pone.0011147openalex-snapshot
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
inferredcites →https://doi.org/10.1371/journal.pone.0046415openalex-snapshot
Evaluation of Different Reference Based Annotation Strategies Using RNA-Seq – A Case Study in Drososphila pseudoobscura
inferredcites →https://doi.org/10.1371/journal.pone.0072614openalex-snapshot
DistMap: A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster
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.0132628openalex-snapshot
Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing
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/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

What points at this work

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

inferred← citeshttps://doi.org/10.1093/ve/veab031openalex-snapshot
The discovery, distribution, and diversity of DNA viruses associated withDrosophila melanogasterin Europe
inferred← citeshttps://doi.org/10.1101/2021.08.16.456461openalex-snapshot
Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes
inferred← citeshttps://doi.org/10.1101/gr.263442.120openalex-snapshot
Evolution of genome structure in the Drosophila simulans species complex
inferred← citeshttps://doi.org/10.1111/mec.16311openalex-snapshot
Evolutionary dynamics of piRNA clusters in Drosophila
inferred← citeshttps://doi.org/10.7554/elife.75795openalex-snapshot
Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes
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