ArticlePeerJ2015
NxRepair: error correction in de novo sequence assembly using Nextera mate pairs.
Article in PeerJ, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 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
9 citing papers in PubMed.
- Isolation, Genomic Sequence and Physiological Characterization ofApplied and environmental microbiology · 2023Article
- Draft Genome Sequence ofMicrobiology resource announcements · 2020Article
- Draft Genome Sequences of Two Thermophilic Moorella sp. Strains, Isolated from an Acidic Hot Spring in Japan.Microbiology resource announcements · 2019Article
- Modern technologies and algorithms for scaffolding assembled genomes.PLoS computational biology · 2019Review
- Complete Genome Sequence of Abscisic Acid-Metabolizing RhizobacteriumMicrobiology resource announcements · 2019Article
- Complete genome sequence of the abscisic acid-utilizing strain3 Biotech · 2019Article
- Draft Genome Sequence of Parageobacillus thermoglucosidasius Strain TG4, a Hydrogenogenic Carboxydotrophic Bacterium Isolated from a Marine Sediment.Microbiology resource announcements · 2019Article
- Tigmint: correcting assembly errors using linked reads from large molecules.BMC bioinformatics · 2018Article
- Next Generation Sequencing of Actinobacteria for the Discovery of Novel Natural Products.Marine drugs · 2016Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Scaffolding errors and incorrect repeat disambiguation during de novo assembly can result in large scale misassemblies in draft genomes. Nextera mate pair sequencing data provide additional information to resolve assembly ambiguities during scaffolding. Here, we introduce NxRepair, an open source toolkit for error correction in de novo assemblies that uses Nextera mate pair libraries to identify and correct large-scale errors. We show that NxRepair can identify and correct large scaffolding errors, without use of a reference sequence, resulting in quantitative improvements in the assembly quality. NxRepair can be downloaded from GitHub or PyPI, the Python Package Index; a tutorial and user documentation are also available.
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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.