ArticleBioinformatics (Oxford, England)2014
De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
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- Genome sequence of a multidrug-resistant Campylobacter coli strain isolated from a newborn with severe diarrhea in Lebanon.Folia microbiologica · 2022Article
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- A bioinformatic platform to integrate target capture and whole genome sequences of various read depths for phylogenomics.Molecular ecology · 2021Article
- 12/111phiA Prophage Domestication Is Associated with Autoaggregation and Increased Ability to Produce Biofilm inMicroorganisms · 2021Article
- Whole-Genome Epidemiology and Characterization of Methicillin-SusceptibleFrontiers in microbiology · 2021Article
- Stem rust resistance in wheat is suppressed by a subunit of the mediator complex.Nature communications · 2020Article
- Bacterial SBP56 identified as a Cu-dependent methanethiol oxidase widely distributed in the biosphere.The ISME journal · 2018Article
- Impact of Exposure of Methicillin-Resistant Staphylococcus aureus to PolyhexanideAntimicrobial agents and chemotherapy · 2017Article
- A Clostridium difficile Lineage Endemic to Costa Rican Hospitals Is Multidrug Resistant by Acquisition of Chromosomal Mutations and Novel Mobile Genetic Elements.Antimicrobial agents and chemotherapy · 2017Article
- Complete Genome Sequence ofGenome announcements · 2017Article
- Prophages and adaptation of Staphylococcus aureus ST398 to the human clinic.BMC genomics · 2017Article
- Draft Genome Sequence of Hypervirulent and Vaccine Candidate Streptococcus suis Strain SC19.Genome announcements · 2017Article
- A Potential New Human Pathogen Belonging toFrontiers in microbiology · 2017Article
- BASE: a practical de novo assembler for large genomes using long NGS reads.BMC genomics · 2016Article
- Draft Genome Sequence of Aeromonas sp. Strain EERV15.Genome announcements · 2016Article
- Draft Genome Sequence of Methylobacterium sp. Strain ARG-1 Isolated from the White-Rot Fungus Armillaria gallica.Genome announcements · 2016Article
- GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research.PLoS computational biology · 2016Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
motivationPaired-end sequencing allows circumventing the shortness of the reads produced by second generation sequencers and is essential for de novo assembly of genomes. However, obtaining a finished genome from short reads is still an open challenge. We present an algorithm that exploits the pairing information issued from inserts of potentially any length. The method determines paths through an overlaps graph by using a constrained search tree. We also present a method that automatically determines suited overlaps cutoffs according to the contextual coverage, reducing thus the need for manual parameterization. Finally, we introduce an interactive mode that allows querying an assembly at targeted regions.
resultsWe assess our methods by assembling two Staphylococcus aureus strains that were sequenced on the Illumina platform. Using 100 bp paired-end reads and minimal manual curation, we produce a finished genome sequence for the previously undescribed isolate SGH-10-168. AVAILABILITY AND IMPLEMENTATION: The presented algorithms are implemented in the standalone Edena software, freely available under the General Public License (GPLv3) at www.genomic.ch/edena.php.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.