ArticleBioinformatics (Oxford, England)2010
Integrating genome assemblies with MAIA.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- A high-quality reference genome for the fish pathogenMicrobial genomics · 2022Article
- Yeast Assimilable Nitrogen Concentrations Influence Yeast Gene Expression and Hydrogen Sulfide Production During Cider Fermentation.Frontiers in microbiology · 2020Article
- MAC: Merging Assemblies by Using Adjacency Algebraic Model and Classification.Frontiers in genetics · 2019Article
- CAMSA: a tool for comparative analysis and merging of scaffold assemblies.BMC bioinformatics · 2017Article
- Single molecule sequencing-guided scaffolding and correction of draft assemblies.BMC genomics · 2017Article
- Nanopore sequencing enables near-complete de novo assembly of Saccharomyces cerevisiae reference strain CEN.PK113-7D.FEMS yeast research · 2017Article
- A comparative evaluation of genome assembly reconciliation tools.Genome biology · 2017Article
- ScaffoldScaffolder: solving contig orientation via bidirected to directed graph reduction.Bioinformatics (Oxford, England) · 2016Article
- Metassembler: merging and optimizing de novo genome assemblies.Genome biology · 2015Article
- De novo meta-assembly of ultra-deep sequencing data.Bioinformatics (Oxford, England) · 2015Article
- Improved assemblies using a source-agnostic pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of contigs.Scientific reports · 2014Article
- A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data.PLoS computational biology · 2014Article
- GAGE-B: an evaluation of genome assemblers for bacterial organisms.Bioinformatics (Oxford, England) · 2013Article
- Next-generation sequence assembly: four stages of data processing and computational challenges.PLoS computational biology · 2013Review
- Graphical contig analyzer for all sequencing platforms (G4ALL): a new stand-alone tool for finishing and draft generation of bacterial genomes.Bioinformation · 2013Article
- GAM-NGS: genomic assemblies merger for next generation sequencing.BMC bioinformatics · 2013Article
- Article
- Finishing bacterial genome assemblies with Mix.BMC bioinformatics · 2013Article
- De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology.Microbial cell factories · 2012Article
- Genome-wide analytical approaches for reverse metabolic engineering of industrially relevant phenotypes in yeast.FEMS yeast research · 2012Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationDe novo assembly of a eukaryotic genome with next-generation sequencing data is still a challenging task. Over the past few years several assemblers have been developed, often suitable for one specific type of sequencing data. The number of known genomes is expanding rapidly, therefore it becomes possible to use multiple reference genomes for assembly projects. We introduce an assembly integrator that makes use of all available data, i.e. multiple de novo assemblies and mappings against multiple related genomes, by optimizing a weighted combination of criteria.
resultsThe developed algorithm was applied on the de novo sequencing of the Saccharomyces cerevisiae CEN.PK 113-7D strain. Using Solexa and 454 read data, two de novo and three comparative assemblies were constructed and subsequently integrated, yielding 29 contigs, covering more than 12 Mbp; a drastic improvement compared with the single assemblies. AVAILABILITY: MAIA is available as a Matlab package and can be downloaded from http://bioinformatics.tudelft.nl.
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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.