ArticleBMC bioinformatics2013
Finishing bacterial genome assemblies with Mix.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Veronia nyctiphanis gen. nov., sp. nov., Isolated from the Stomach of the Euphausiid Nyctiphanes simplex (Hansen, 1911) in the Gulf of California, and Reclassification of Enterovibrio pacificus as Veronia pacifica comb. nov.Current microbiology · 2021Article
- Genomic analysis reveals the potential for hydrocarbon degradation of Rhodopirellula sp. MGV isolated from a polluted Brazilian mangrove.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2021Article
- Phylogenomic Analysis Supports Two Possible Origins for Latin American Strains of Vibrio parahaemolyticus Associated with Acute Hepatopancreatic Necrosis Disease (AHPND).Current microbiology · 2020Article
- Localized effect of treated wastewater effluent on the resistome of an urban watershed.GigaScience · 2020Article
- TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers.Genome research · 2020Article
- Photobacterium lucens sp. nov., Isolated from a Cultured Shrimp Penaeus vannamei.Current microbiology · 2020Article
- MAC: Merging Assemblies by Using Adjacency Algebraic Model and Classification.Frontiers in genetics · 2019Article
- Novo&Stitch: accurate reconciliation of genome assemblies via optical maps.Bioinformatics (Oxford, England) · 2018Article
- Draft genome sequences ofStandards in genomic sciences · 2018Article
- A comparative evaluation of genome assembly reconciliation tools.Genome biology · 2017Article
- Draft Genome Sequence of Deep-Sea Alteromonas sp. Strain V450 Isolated from the Marine Sponge Leiodermatium sp.Genome announcements · 2017Article
- The draft genome of the hyperthermophilic archaeonStandards in genomic sciences · 2017Article
- Presence of Apis Rhabdovirus-1 in Populations of Pollinators and Their Parasites from Two Continents.Frontiers in microbiology · 2017Article
- Genome Sequence of Fusarium Isolate MYA-4552 from the Midgut of Anoplophora glabripennis, an Invasive, Wood-Boring Beetle.Genome announcements · 2016Article
- Draft Genome Sequence of Hydrotalea flava Strain CCUG 51397T.Genome announcements · 2016Article
- Draft Genome Sequence of a Novel Acidophilic Iron-Oxidizing Firmicutes Species, "Acidibacillus ferrooxidans" (SLC66T).Genome announcements · 2016Article
- Draft Genome Sequence of "Acidibacillus ferrooxidans" ITV01, a Novel Acidophilic Firmicute Isolated from a Chalcopyrite Mine Drainage Site in Brazil.Genome announcements · 2016Article
- Genome Sequence and Analysis of Peptoclostridium difficile Strain ZJCDC-S82.Evolutionary bioinformatics online · 2016Article
- De novo meta-assembly of ultra-deep sequencing data.Bioinformatics (Oxford, England) · 2015Article
- Draft Genome Sequence of the Nicotinate-Metabolizing Soil Bacterium Bacillus niacini DSM 2923.Genome announcements · 2014Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationAmong challenges that hamper reaping the benefits of genome assembly are both unfinished assemblies and the ensuing experimental costs. First, numerous software solutions for genome de novo assembly are available, each having its advantages and drawbacks, without clear guidelines as to how to choose among them. Second, these solutions produce draft assemblies that often require a resource intensive finishing phase.
methodsIn this paper we address these two aspects by developing Mix , a tool that mixes two or more draft assemblies, without relying on a reference genome and having the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a set of paths in the extension graph that maximizes the cumulative contig length.
resultsWe evaluate the performance of Mix on bacterial NGS data from the GAGE-B study and apply it to newly sequenced Mycoplasma genomes. Resulting final assemblies demonstrate a significant improvement in the overall assembly quality. In particular, Mix is consistent by providing better overall quality results even when the choice is guided solely by standard assembly statistics, as is the case for de novo projects. AVAILABILITY: Mix is implemented in Python and is available at https://github.com/cbib/MIX, novel data for our Mycoplasma study is available at http://services.cbib.u-bordeaux2.fr/mix/.
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