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Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler

https://doi.org/10.1371/journal.pone.0008407

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What this work says

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

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Applied Biosystems SOLiD™ System: Ligation‐Based Sequencing

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Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads

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Fragment assembly with double-barreled data

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The fragment assembly string graph

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Assembling millions of short DNA sequences using SSAKE

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Extending assembly of short DNA sequences to handle error

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An analysis of the feasibility of short read sequencing

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De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer

inferredcites →https://doi.org/10.1101/gr.074492.107openalex-snapshot

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

inferredcites →https://doi.org/10.1101/gr.079053.108openalex-snapshot

De novo fragment assembly with short mate-paired reads: Does the read length matter?

inferredcites →https://doi.org/10.1101/gr.089532.108openalex-snapshot

ABySS: A parallel assembler for short read sequence data

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Hierarchical Scaffolding With Bambus

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High-Throughput Gene Mapping in Caenorhabditis elegans

inferredcites →https://doi.org/10.1101/gr.6435207openalex-snapshot

SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing

inferredcites →https://doi.org/10.1101/gr.7088808openalex-snapshot

Short read fragment assembly of bacterial genomes

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Human–Mouse Alignments with BLASTZ

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Crystallizing short-read assemblies around seeds

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MetaVelvet

inferred← citeshttps://doi.org/10.1186/1471-2105-12-354openalex-snapshot

Parallelized short read assembly of large genomes using de Bruijn graphs

inferred← citeshttps://doi.org/10.1186/1471-2105-12-95openalex-snapshot

Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies

inferred← citeshttps://doi.org/10.1186/1471-2105-14-s11-s5openalex-snapshot

A base composition analysis of natural patterns for the preprocessing of metagenome sequences

inferred← citeshttps://doi.org/10.1186/1471-2164-12-569openalex-snapshot

Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection

inferred← citeshttps://doi.org/10.1186/1471-2164-13-268openalex-snapshot

Genome characterisation of the genus Francisella reveals insight into similar evolutionary paths in pathogens of mammals and fish

inferred← citeshttps://doi.org/10.1186/1471-2164-13-474openalex-snapshot

RNA-Seq reveals complex genetic response to deepwater horizon oil release in Fundulus grandis

inferred← citeshttps://doi.org/10.1186/1471-2164-13-492openalex-snapshot

Transcriptome-scale homoeolog-specific transcript assemblies of bread wheat

inferred← citeshttps://doi.org/10.1186/1471-2164-14-320openalex-snapshot

Sequencing platform and library preparation choices impact viral metagenomes

inferred← citeshttps://doi.org/10.1186/1471-2164-14-91openalex-snapshot

Global analyses of Ceratocystis cacaofunesta mitochondria: from genome to proteome

inferred← citeshttps://doi.org/10.1186/1471-2164-15-699openalex-snapshot

Performance comparison of second- and third-generation sequencers using a bacterial genome with two chromosomes

inferred← citeshttps://doi.org/10.1186/1752-0509-7-s6-s7openalex-snapshot

OMACC: an Optical-Map-Assisted Contig Connector for improving de novo genome assembly

inferred← citeshttps://doi.org/10.1186/1755-8794-8-s3-s5openalex-snapshot

Hybrid de novo tandem repeat detection using short and long reads

inferred← citeshttps://doi.org/10.1186/1756-0500-5-243openalex-snapshot

Arapan-S: a fast and highly accurate whole-genome assembly software for viruses and small genomes

inferred← citeshttps://doi.org/10.1186/2042-5783-3-2openalex-snapshot

Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data

inferred← citeshttps://doi.org/10.1186/gb-2010-11-1-202openalex-snapshot

Assembling genomes using short-read sequencing technology

inferred← citeshttps://doi.org/10.1186/s12859-015-0705-yopenalex-snapshot

WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data

inferred← citeshttps://doi.org/10.1186/s12859-015-0801-zopenalex-snapshot

An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome

inferred← citeshttps://doi.org/10.1186/s12864-018-4440-4openalex-snapshot

Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC)

inferred← citeshttps://doi.org/10.1186/s13059-015-0596-2openalex-snapshot

Bridger: a new framework for de novo transcriptome assembly using RNA-seq data

inferred← citeshttps://doi.org/10.1186/s13059-018-1539-5openalex-snapshot

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

inferred← citeshttps://doi.org/10.1266/ggs.21-00052openalex-snapshot

Development of microsatellite markers for the mycoheterotrophic species Burmannia nepalensis (Miers) Hook.f. based on RAD sequencing

inferred← citeshttps://doi.org/10.12688/f1000research.164600.1openalex-snapshot

Characterization of red pigmented yeasts and genes associated with astaxanthin synthesis in Rhodotorula mucilaginosa HL26-1 and Rhodotorula paludigena LL69-1

inferred← citeshttps://doi.org/10.13025/17203openalex-snapshot

Fuzzy k-mers and their application to comparative genome assembly

inferred← citeshttps://doi.org/10.1371/journal.pbio.1001156openalex-snapshot

ESRRA-C11orf20 Is a Recurrent Gene Fusion in Serous Ovarian Carcinoma

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1003345openalex-snapshot

Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1006994openalex-snapshot

Modern technologies and algorithms for scaffolding assembled genomes

inferred← citeshttps://doi.org/10.1371/journal.pone.0017915openalex-snapshot

A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies

inferred← citeshttps://doi.org/10.1371/journal.pone.0019175openalex-snapshot

Comparing De Novo Genome Assembly: The Long and Short of It

inferred← citeshttps://doi.org/10.1371/journal.pone.0023501openalex-snapshot

Meraculous: De Novo Genome Assembly with Short Paired-End Reads

inferred← citeshttps://doi.org/10.1371/journal.pone.0043359openalex-snapshot

An Improved Protocol for Sequencing of Repetitive Genomic Regions and Structural Variations Using Mutagenesis and Next Generation Sequencing

inferred← citeshttps://doi.org/10.1371/journal.pone.0053525openalex-snapshot

A Genome-Wide Association Study Identifies Genomic Regions for Virulence in the Non-Model Organism Heterobasidion annosum s.s

inferred← citeshttps://doi.org/10.1371/journal.pone.0061190openalex-snapshot

Transcriptome of the Lymantria dispar (Gypsy Moth) Larval Midgut in Response to Infection by Bacillus thuringiensis

inferred← citeshttps://doi.org/10.1371/journal.pone.0062856openalex-snapshot

Effects of GC Bias in Next-Generation-Sequencing Data on De Novo Genome Assembly

inferred← citeshttps://doi.org/10.1371/journal.pone.0089235openalex-snapshot

Whole Genome Analysis of a Community-Associated Methicillin-Resistant Staphylococcus aureus ST59 Isolate from a Case of Human Sepsis and Severe Pneumonia in China

inferred← citeshttps://doi.org/10.1371/journal.pone.0103567openalex-snapshot

De Novo Assembly of the Perennial Ryegrass Transcriptome Using an RNA-Seq Strategy

inferred← citeshttps://doi.org/10.1371/journal.pone.0107854openalex-snapshot

Conserved Gene Order and Expanded Inverted Repeats Characterize Plastid Genomes of Thalassiosirales

inferred← citeshttps://doi.org/10.1371/journal.pone.0140749openalex-snapshot

A Non-Synonymous HMGA2 Variant Decreases Height in Shetland Ponies and Other Small Horses

inferred← citeshttps://doi.org/10.1371/journal.pone.0304699openalex-snapshot

Comparative genomic analysis and optimization of astaxanthin production of Rhodotorula paludigena TL35-5 and Rhodotorula sampaioana PL61-2

inferred← citeshttps://doi.org/10.1371/journal.ppat.1006252openalex-snapshot

Genomic and phenotypic characterization of myxoma virus from Great Britain reveals multiple evolutionary pathways distinct from those in Australia

inferred← citeshttps://doi.org/10.1653/024.100.0422openalex-snapshot

Morganella morganii(Enterobacteriales: Enterobacteriaceae) Is a Lethal Pathogen of Mexican Fruit Fly (Diptera: Tephritidae) Larvae

inferred← citeshttps://doi.org/10.2147/idr.s35710openalex-snapshot

Whole-genome sequencing in bacteriology: state of the art

inferred← citeshttps://doi.org/10.2217/pgs.12.72openalex-snapshot

Next-Generation Sequencing and Large Genome Assemblies

inferred← citeshttps://doi.org/10.25335/41j2-ha60openalex-snapshot

Identification of candidate genes and isoforms associated with genetic resistance to Marek's disease from RNA-Seq data

inferred← citeshttps://doi.org/10.26512/2018.02.d.32803openalex-snapshot

Caracterização do carlavírus Melon yellowing-associated virus e do polerovírus Cucurbit aphid-borne yellows virus em meloeiro

inferred← citeshttps://doi.org/10.26686/wgtn.17007808openalex-snapshot

Molecular characterization of bacterial diversity in New Zealand groundwater

inferred← citeshttps://doi.org/10.26686/wgtn.17007808.v1openalex-snapshot

Molecular characterization of bacterial diversity in New Zealand groundwater

inferred← citeshttps://doi.org/10.3389/fbioe.2020.00974openalex-snapshot

Cobetia sp. Bacteria, Which Are Capable of Utilizing Alginate or Waste Laminaria sp. for Poly(3-Hydroxybutyrate) Synthesis, Isolated From a Marine Environment

inferred← citeshttps://doi.org/10.3389/fmicb.2018.02981openalex-snapshot

Viral Diversity and Its Relationship With Environmental Factors at the Surface and Deep Sea of Prydz Bay, Antarctica

inferred← citeshttps://doi.org/10.3389/fmicb.2021.710262openalex-snapshot

Genomic Changes and Genetic Divergence of Vibrio alginolyticus Under Phage Infection Stress Revealed by Whole-Genome Sequencing and Resequencing

inferred← citeshttps://doi.org/10.3389/fmicb.2022.939919openalex-snapshot

Complete genome sequencing and in silico genome mining reveal the promising metabolic potential in Streptomyces strain CS-7

inferred← citeshttps://doi.org/10.3389/fmicb.2024.1385860openalex-snapshot

Isolation and identification of specific Enterococcus faecalis phage C-3 and G21-7 against Avian pathogenic Escherichia coli and its application to one-day-old geese

inferred← citeshttps://doi.org/10.3389/fmicb.2024.1407039openalex-snapshot

Genomic and biological insights of bacteriophages JNUWH1 and JNUWD in the arms race against bacterial resistance

inferred← citeshttps://doi.org/10.3389/fmicb.2026.1791000openalex-snapshot

Clinical significance and simultaneous microevolution of two closely-related nontuberculous mycobacteria species

inferred← citeshttps://doi.org/10.3389/fphys.2019.00977openalex-snapshot

A Vaccinomics Approach for the Identification of Tick Protective Antigens for the Control of Ixodes ricinus and Dermacentor reticulatus Infestations in Companion Animals

inferred← citeshttps://doi.org/10.3389/fpls.2015.00241openalex-snapshot

Comprehensive analysis of transcriptome response to salinity stress in the halophytic turf grass Sporobolus virginicus

inferred← citeshttps://doi.org/10.3390/antibiotics15030235openalex-snapshot

Comparative Genomic and Epidemiologic Analysis of Methicillin-Resistant Staphylococcus aureus Isolates in Republic of Korea

inferred← citeshttps://doi.org/10.3390/fermentation10090459openalex-snapshot

Unveiling Acetobacter syzygii from Tibetan Kefir Grain: Fermentation-Enhanced Anti-Tyrosinase, and Anti-Melanin

inferred← citeshttps://doi.org/10.3390/fermentation12010027openalex-snapshot

A Novel Mycoprotein Candidate: Neurospora intermedia FF171 from Pu-Erh Tea with Genomics-Based Safety Profiling

inferred← citeshttps://doi.org/10.3390/fermentation9060501openalex-snapshot

Genomic Insight and Optimization of Astaxanthin Production from a New Rhodotorula sp. CP72-2

inferred← citeshttps://doi.org/10.3390/foods14162850openalex-snapshot

A Novel Lytic Salmonella Phage Harboring an Unprecedented Tail-Protein Domain Combination Capable of Lysing Cross-Host-Transmitted Salmonella Strains

inferred← citeshttps://doi.org/10.3390/microorganisms14010160openalex-snapshot

Accelerated Genomic Evolution and Divergence of Escherichia coli Under Phage Infection Stress: Emphasizing the Role of IS Elements in Changing Genetic Structure

inferred← citeshttps://doi.org/10.3390/v15020455openalex-snapshot

Characterisation of the Upper Respiratory Tract Virome of Feedlot Cattle and Its Association with Bovine Respiratory Disease

inferred← citeshttps://doi.org/10.3732/apps.1400101openalex-snapshot

Isolation and characterization of 22 EST‐SSR markers for the genus Thujopsis (Cupressaceae)

inferred← citeshttps://doi.org/10.4304/jsw.9.8.2160-2168openalex-snapshot

De Bruijn Graph based De novo Genome Assembly

inferred← citeshttps://doi.org/10.47749/t/unicamp.2013.884744openalex-snapshot

Análise do genoma da microalga produtora de lipídios Neochloris oleoabundans,visando à produção de combustíveis de terceira geração

inferred← citeshttps://doi.org/10.48550/arxiv.1307.0541openalex-snapshot

A hierarchical network heuristic for solving the orientation problem in genome assembly

inferred← citeshttps://doi.org/10.48550/arxiv.1307.7642openalex-snapshot

The genome of the medieval Black Death agent (extended abstract)

inferred← citeshttps://doi.org/10.5109/1957499openalex-snapshot

Editorial

inferred← citeshttps://doi.org/10.5353/th_b5053405openalex-snapshot

Iterative de Bruijn graph assemblers for second-generation sequencing reads

inferred← citeshttps://doi.org/10.53846/goediss-9608openalex-snapshot

Computational methods for de novo assembly and sequencing error correction of short reads in the era of (viral) metagenomics

inferred← citeshttps://doi.org/10.5423/rpd.2014.20.3.216openalex-snapshot

Draft Genome Sequence of a Chitinase-Producing Biocontrol Bacterium, Lysobacter antibioticus HS124

inferred← citeshttps://doi.org/10.5423/rpd.2015.21.3.222openalex-snapshot

Draft Genome Sequence of a Chitinase-producing Biocontrol Bacterium Serratia sp. C-1

inferred← citeshttps://doi.org/10.70675/98efd384zdb06z4edez89c2z7207630ad7aaopenalex-snapshot

Systématique, phylogénie et évolution moléculaires des Phyllostomidae (Mammalia, Chiroptera) : une approche mitogénomique comparative

inferred← citeshttps://doi.org/10.70675/f8e1699bz5c09z4cbbzaaf2z826bdc03cd43openalex-snapshot

Rôle des protistes hétérotrophes marins dans le cycle du carbone océanique par génomique en cellule unique

showing the first 200 of 206

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.