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Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies
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What this work says
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inferred← citeshttps://doi.org/10.1038/sdata.2018.69openalex-snapshot
The draft genome sequence of cork oak
inferred← citeshttps://doi.org/10.1038/srep21016openalex-snapshot
Comparative genomics of mitochondria in chlorarachniophyte algae: endosymbiotic gene transfer and organellar genome dynamics
inferred← citeshttps://doi.org/10.1038/srep22262openalex-snapshot
Resolving evolutionary relationships in lichen-forming fungi using diverse phylogenomic datasets and analytical approaches
inferred← citeshttps://doi.org/10.1038/srep36089openalex-snapshot
Mitochondrial genomes and comparative genomics of Aphanomyces astaci and Aphanomyces invadans
inferred← citeshttps://doi.org/10.1038/srep40455openalex-snapshot
Unraveling the microbial processes of black band disease in corals through integrated genomics
inferred← citeshttps://doi.org/10.1055/s-0033-1361817openalex-snapshot
Use of Whole Genome Shotgun Metagenomics: A Practical Guide for the Microbiome-Minded Physician Scientist
inferred← citeshttps://doi.org/10.1073/pnas.1205020109openalex-snapshot
Gain and loss of multiple functionally related, horizontally transferred genes in the reduced genomes of two microsporidian parasites
inferred← citeshttps://doi.org/10.1073/pnas.1304322110openalex-snapshot
Hammondia hammondi , an avirulent relative of Toxoplasma gondii , has functional orthologs of known T. gondii virulence genes
inferred← citeshttps://doi.org/10.1073/pnas.1412277112openalex-snapshot
Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris
inferred← citeshttps://doi.org/10.1073/pnas.1421391112openalex-snapshot
Maternal transmission, sex ratio distortion, and mitochondria
inferred← citeshttps://doi.org/10.1073/pnas.1603910113openalex-snapshot
Repeated replacement of an intrabacterial symbiont in the tripartite nested mealybug symbiosis
inferred← citeshttps://doi.org/10.1073/pnas.1613375114openalex-snapshot
Multiple horizontal transfers of nuclear ribosomal genes between phylogenetically distinct grass lineages
inferred← citeshttps://doi.org/10.1080/23802359.2017.1310610openalex-snapshot
The complete chloroplast genome of the green microalgae Dunaliella salina strain SQ
inferred← citeshttps://doi.org/10.1080/23802359.2017.1331331openalex-snapshot
The complete mitochondrial genome of the green microalgae Dunaliella salina strain SQ
inferred← citeshttps://doi.org/10.1080/23802359.2017.1347838openalex-snapshot
Complete chloroplast genomes of the Chlamydomonas reinhardtii nonphotosynthetic mutants CC-1375, CC-373, CC-4199, CC-2359 and CC-1051
inferred← citeshttps://doi.org/10.1080/23802359.2017.1361357openalex-snapshot
The complete mitochondrial genome of the copepodCalanus glacialis
inferred← citeshttps://doi.org/10.1080/23802359.2017.1407685openalex-snapshot
The complete mitochondrial genome of the scorpion Centruroides vittatus (Arachnida: Scorpiones)
inferred← citeshttps://doi.org/10.1080/23802359.2017.1407704openalex-snapshot
Mitochondrial genome of Dinophilus gyrociliatus (Annelida: Dinophilidae)
inferred← citeshttps://doi.org/10.1080/23802359.2018.1462126openalex-snapshot
The complete mitochondrial DNA of the tropical oyster Crassostrea belcheri from the Cần Giò’ mangrove in Vietnam
inferred← citeshttps://doi.org/10.1080/23802359.2018.1535852openalex-snapshot
Complete mitochondrial genome of a rare diatom (Bacillariophyta) Proschkinia and its phylogenetic and taxonomic implications
inferred← citeshttps://doi.org/10.1080/23802359.2018.1544043openalex-snapshot
Mitochondrial genome of Parborlasia corrugatus (Nemertea: Lineidae)
inferred← citeshttps://doi.org/10.1080/23802359.2019.1617049openalex-snapshot
The complete mitogenome of Sydowia polyspora
inferred← citeshttps://doi.org/10.1080/23802359.2019.1693300openalex-snapshot
Complete mitogenome of the streptophyte green alga Coleochaete scutata (Coleochaetophyceae)
inferred← citeshttps://doi.org/10.1080/23802359.2020.1844094openalex-snapshot
The complete mitogenome of Diaporthe nobilis
inferred← citeshttps://doi.org/10.1086/bblv225n3p194openalex-snapshot
Hemichordate Molecular Phylogeny Reveals a Novel Cold-Water Clade of Harrimaniid Acorn Worms
inferred← citeshttps://doi.org/10.1089/big.2013.0031openalex-snapshot
Human Analysts at Superhuman Scales: What Has Friendly Software To Do?
inferred← citeshttps://doi.org/10.1089/cmb.2013.0084openalex-snapshot
Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products
inferred← citeshttps://doi.org/10.1089/cmb.2016.0141openalex-snapshot
Safe and Complete Contig Assembly Through Omnitigs
inferred← citeshttps://doi.org/10.1089/cmb.2017.0250openalex-snapshot
Fast Metagenomic Binning via Hashing and Bayesian Clustering
inferred← citeshttps://doi.org/10.1089/cmb.2022.0261openalex-snapshot
Improving RNA Assembly via Safety and Completeness in Flow Decompositions
inferred← citeshttps://doi.org/10.1089/phage.2021.0015openalex-snapshot
Phage Genome Annotation: Where to Begin and End
inferred← citeshttps://doi.org/10.1093/bfgp/elr042openalex-snapshot
Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics
inferred← citeshttps://doi.org/10.1093/bib/bbz025openalex-snapshot
Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences
inferred← citeshttps://doi.org/10.1093/bioinformatics/btt590openalex-snapshot
De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads
inferred← citeshttps://doi.org/10.1093/bioinformatics/btu266openalex-snapshot
ExSPAnder: a universal repeat resolver for DNA fragment assembly
inferred← citeshttps://doi.org/10.1093/bioinformatics/btv226openalex-snapshot
De novo meta-assembly of ultra-deep sequencing data
inferred← citeshttps://doi.org/10.1093/bioinformatics/btv337openalex-snapshot
Assembling short reads from jumping libraries with large insert sizes
inferred← citeshttps://doi.org/10.1093/bioinformatics/btv688openalex-snapshot
hybrid SPA des : an algorithm for hybrid assembly of short and long reads
inferred← citeshttps://doi.org/10.1093/bioinformatics/btw279openalex-snapshot
Compacting de Bruijn graphs from sequencing data quickly and in low memory
inferred← citeshttps://doi.org/10.1093/bioinformatics/btx808openalex-snapshot
Analyzing large scale genomic data on the cloud with Sparkhit
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty479openalex-snapshot
panISa: ab initio detection of insertion sequences in bacterial genomes from short read sequence data
inferred← citeshttps://doi.org/10.1093/bioinformatics/btz072openalex-snapshot
Assembly Graph Browser: interactive visualization of assembly graphs
inferred← citeshttps://doi.org/10.1093/database/bay027openalex-snapshot
Maser: one-stop platform for NGS big data from analysis to visualization
inferred← citeshttps://doi.org/10.1093/femsle/fnw049openalex-snapshot
MEGAnnotator: a user-friendly pipeline for microbial genomes assembly and annotation
inferred← citeshttps://doi.org/10.1093/femsle/fnw263openalex-snapshot
Genix: a new online automated pipeline for bacterial genome annotation
inferred← citeshttps://doi.org/10.1093/gbe/evab215openalex-snapshot
Plastome Structural Evolution and Homoplastic Inversions in Neo-Astragalus (Fabaceae)
inferred← citeshttps://doi.org/10.1093/gbe/evac089openalex-snapshot
Contrasting Modes of Mitochondrial Genome Evolution in Sister Taxa of Wood-Eating Marine Bivalves (Teredinidae and Xylophagaidae)
inferred← citeshttps://doi.org/10.1093/gbe/evt122openalex-snapshot
Palindromic Genes in the Linear Mitochondrial Genome of the Nonphotosynthetic Green Alga Polytomella magna
inferred← citeshttps://doi.org/10.1093/gbe/evt159openalex-snapshot
Phylogenetic Diversity of the Enteric Pathogen Salmonella enterica subsp. enterica Inferred from Genome-Wide Reference-Free SNP Characters
inferred← citeshttps://doi.org/10.1093/gbe/evu039openalex-snapshot
Serial Gene Losses and Foreign DNA Underlie Size and Sequence Variation in the Plastid Genomes of Diatoms
inferred← citeshttps://doi.org/10.1093/gbe/evu218openalex-snapshot
The Mitochondrial Genomes of the Glaucophytes Gloeochaete wittrockiana and Cyanoptyche gloeocystis: Multilocus Phylogenetics Suggests a Monophyletic Archaeplastida
inferred← citeshttps://doi.org/10.1093/gbe/evv027openalex-snapshot
Massive and Widespread Organelle Genomic Expansion in the Green Algal Genus Dunaliella
inferred← citeshttps://doi.org/10.1093/gbe/evw190openalex-snapshot
Mitochondrion-to-Chloroplast DNA Transfers and Intragenomic Proliferation of Chloroplast Group II Introns inGloeotilopsisGreen Algae (Ulotrichales, Ulvophyceae)
inferred← citeshttps://doi.org/10.1093/gbe/evx086openalex-snapshot
Mitochondrial Genome Evolution and a Novel RNA Editing System in Deep-Branching Heteroloboseids
inferred← citeshttps://doi.org/10.1093/gbe/evy254openalex-snapshot
Mitogenomics Reveals a Novel Genetic Code in Hemichordata
inferred← citeshttps://doi.org/10.1093/gbe/evy268openalex-snapshot
Plastid Genomes from Diverse Glaucophyte Genera Reveal a Largely Conserved Gene Content and Limited Architectural Diversity
inferred← citeshttps://doi.org/10.1093/gbe/evz119openalex-snapshot
The Population Structure of Pseudomonas aeruginosa Is Characterized by Genetic Isolation of exoU+ and exoS+ Lineages
inferred← citeshttps://doi.org/10.1093/gbe/evz229openalex-snapshot
The Mitochondrial Genome of Eleusine indica and Characterization of Gene Content Within Poaceae
inferred← citeshttps://doi.org/10.1093/gbe/evz270openalex-snapshot
Microsporidia with Vertical Transmission Were Likely Shaped by Nonadaptive Processes
inferred← citeshttps://doi.org/10.1093/gigascience/giae038openalex-snapshot
gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes
inferred← citeshttps://doi.org/10.1093/gigascience/giy098openalex-snapshot
Bioinformatics applications on Apache Spark
inferred← citeshttps://doi.org/10.1093/jacamr/dlad026openalex-snapshot
Characterization of vancomycin-resistancevanDgene clusters in the human intestinal microbiota by metagenomics and culture-enriched metagenomics
inferred← citeshttps://doi.org/10.1093/jcbiol/ruad028openalex-snapshot
First mitochondrial genomes of Anaspidacea (Malacostraca, Crustacea) and the phylogenetic relationships of mountain shrimps (AnaspidesThomson, 1894) and their relatives within Anaspidesidae
inferred← citeshttps://doi.org/10.1093/jpids/piz032openalex-snapshot
Prospective Cohort Study of Next-Generation Sequencing as a Diagnostic Modality for Unexplained Encephalitis in Children
inferred← citeshttps://doi.org/10.1093/jxb/erz136openalex-snapshot
Nitric oxide-dependent regulation of sweet pepper fruit ripening
inferred← citeshttps://doi.org/10.1093/molbev/msab026openalex-snapshot
Genome-Scale Profiling Reveals Noncoding Loci Carry Higher Proportions of Concordant Data
inferred← citeshttps://doi.org/10.1093/molbev/msae055openalex-snapshot
Fermentation Practices Select for Thermostable Endolysins in Phages
inferred← citeshttps://doi.org/10.1093/molbev/msaf111openalex-snapshot
Relaxed Purifying Selection is Associated with an Accumulation of Transposable Elements in Flies
inferred← citeshttps://doi.org/10.1093/molbev/mst002openalex-snapshot
Organelle Genome Complexity Scales Positively with Organism Size in Volvocine Green Algae
inferred← citeshttps://doi.org/10.1093/molbev/msw126openalex-snapshot
Genome-Wide Survey of Gut Fungi (Harpellales) Reveals the First Horizontally Transferred Ubiquitin Gene from a Mosquito Host
inferred← citeshttps://doi.org/10.1093/molbev/msx200openalex-snapshot
Phenetic Comparison of Prokaryotic Genomes Using k-mers
inferred← citeshttps://doi.org/10.1093/nar/gkad406openalex-snapshot
WebQUAST: online evaluation of genome assemblies
inferred← citeshttps://doi.org/10.1093/nar/gkr834openalex-snapshot
Genome sequencing of the lizard parasite Leishmania tarentolae reveals loss of genes associated to the intracellular stage of human pathogenic species
inferred← citeshttps://doi.org/10.1093/sysbio/syac019openalex-snapshot
A Genomic Perspective on the Evolutionary Diversification of Turtles
inferred← citeshttps://doi.org/10.1093/ve/veaa018openalex-snapshot
Novel genome sequences of cell-fusing agent virus allow comparison of virus phylogeny with the genetic structure of Aedes aegypti populations
inferred← citeshttps://doi.org/10.1093/ve/veaf055openalex-snapshot
Revealing the potential transmission route of Cnaphalocrocis medinalis granulovirus capable of persistently causing granulosis epidemics
inferred← citeshttps://doi.org/10.1098/rsob.150239openalex-snapshot
Moramonas marocensis gen. nov., sp. nov.: a jakobid flagellate isolated from desert soil with a bacteria-like, but bloated mitochondrial genome
inferred← citeshttps://doi.org/10.1099/mic.0.058560-0openalex-snapshot
Extensive variation in surface lipoprotein gene content and genomic changes associated with virulence during evolution of a novel North American house finch epizootic strain of Mycoplasma gallisepticum
inferred← citeshttps://doi.org/10.1099/vir.0.066951-0openalex-snapshot
Novel gammaherpesvirus functions encoded by bovine herpesvirus 6 (bovine lymphotropic virus)
inferred← citeshttps://doi.org/10.1101/005900openalex-snapshot
Complete plastid genome assembly of invasive plant, Centaurea diffusa
inferred← citeshttps://doi.org/10.1101/2020.12.08.416024openalex-snapshot
A Draft Genome for Hirudo verbana , the Medicinal Leech
inferred← citeshttps://doi.org/10.1101/2021.02.02.429443openalex-snapshot
s-aligner: a greedy algorithm for non-greedy de novo genome assembly
inferred← citeshttps://doi.org/10.1101/2021.11.18.469131openalex-snapshot
Interrogating Genomic Data in the Phylogenetic Placement of Treeshrews Reveals Potential Sources of Conflict
inferred← citeshttps://doi.org/10.1101/2023.04.18.537422openalex-snapshot
Exhaustive benchmarking of de novo assembly methods for eukaryotic genomes
inferred← citeshttps://doi.org/10.1101/2023.04.18.537425openalex-snapshot
Pyro: A Comprehensive Pipeline for Eukaryotic Genome Assembly
inferred← citeshttps://doi.org/10.1101/2023.09.27.559745openalex-snapshot
Dairy practices select for thermostable endolysins in phages
inferred← citeshttps://doi.org/10.1101/301903openalex-snapshot
Identification of Significant Computational Building Blocks through Comprehensive Investigation of NGS Secondary Analysis Methods
inferred← citeshttps://doi.org/10.1101/523068openalex-snapshot
PaKman : Scalable Assembly of Large Genomes on Distributed Memory Machines
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