ArticleBioinformatics (Oxford, England)2012
Graph accordance of next-generation sequence assemblies.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
31 citing papers in PubMed.
- TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers.Genome research · 2020Article
- Extensive chromosomal rearrangements and rapid evolution of novel effector superfamilies contribute to host adaptation and speciation in the basal ascomycetous fungi.Molecular plant pathology · 2020Article
- Draft Genome Sequence of Bacillus marisflavi CK-NBRI-03, Isolated from Agricultural Soil.Microbiology resource announcements · 2020Article
- Draft Genome Sequence of a Potential Plant Growth-Promoting Rhizobacterium,Microbiology resource announcements · 2019Article
- MAC: Merging Assemblies by Using Adjacency Algebraic Model and Classification.Frontiers in genetics · 2019Article
- LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly.GigaScience · 2019Article
- Novo&Stitch: accurate reconciliation of genome assemblies via optical maps.Bioinformatics (Oxford, England) · 2018Article
- Article
- The genome of Austrofundulus limnaeus offers insights into extreme vertebrate stress tolerance and embryonic development.BMC genomics · 2018Article
- CAMSA: a tool for comparative analysis and merging of scaffold assemblies.BMC bioinformatics · 2017Article
- A comparative evaluation of genome assembly reconciliation tools.Genome biology · 2017Article
- Whole genome analysis of a schistosomiasis-transmitting freshwater snail.Nature communications · 2017Article
- Article
- A New Chicken Genome Assembly Provides Insight into Avian Genome Structure.G3 (Bethesda, Md.) · 2017Article
- Article
- Article
- A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination.G3 (Bethesda, Md.) · 2016Article
- Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine.Pharmaceutics · 2016Review
- The genome of the vervet (Chlorocebus aethiops sabaeus).Genome research · 2015Article
- InteMAP: Integrated metagenomic assembly pipeline for NGS short reads.BMC bioinformatics · 2015Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
motivationNo individual assembly algorithm addresses all the known limitations of assembling short-length sequences. Overall reduced sequence contig length is the major problem that challenges the usage of these assemblies. We describe an algorithm to take advantages of different assembly algorithms or sequencing platforms to improve the quality of next-generation sequence (NGS) assemblies.
resultsThe algorithm is implemented as a graph accordance assembly (GAA) program. The algorithm constructs an accordance graph to capture the mapping information between the target and query assemblies. Based on the accordance graph, the contigs or scaffolds of the target assembly can be extended, merged or bridged together. Extra constraints, including gap sizes, mate pairs, scaffold order and orientation, are explored to enforce those accordance operations in the correct context. We applied GAA to various chicken NGS assemblies and the results demonstrate improved contiguity statistics and higher genome and gene coverage. AVAILABILITY: GAA is implemented in OO perl and is available here: http://sourceforge.net/projects/gaa-wugi/. CONTACT: lye@genome.wustl.edu
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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.