ArticleBioinformatics (Oxford, England)2021
ARBitR: an overlap-aware genome assembly scaffolder for linked reads.
Article in Bioinformatics (Oxford, England), 2021. 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
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
9 citing papers in PubMed.
- The Bioinformatic Applications of Hi-C and Linked Reads.Genomics, proteomics & bioinformatics · 2024Review
- Whole-genome duplication in an algal symbiont bolsters coral heat tolerance.Science advances · 2024Article
- Comparative genomics of Ascetosporea gives new insight into the evolutionary basis for animal parasitism in Rhizaria.BMC biology · 2024Article
- Genome assembly and annotation of the mermithid nematode Mermis nigrescens.G3 (Bethesda, Md.) · 2024Article
- Massive genome reduction predates the divergence of Symbiodiniaceae dinoflagellates.The ISME journal · 2024Article
- MTG-Link: leveraging barcode information from linked-reads to assemble specific loci.BMC bioinformatics · 2023Article
- Highly accurate genome assembly of an improved high-yielding silkworm strain, Nichi01.G3 (Bethesda, Md.) · 2023Article
- Genome assembly and annotation of the European earwig Forficula auricularia (subspecies B).G3 (Bethesda, Md.) · 2022Article
- The Assembled and Annotated Genome of the Fairy-Ring Fungus Marasmius oreades.Genome biology and evolution · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
summaryLinked genomic sequencing reads contain information that can be used to join sequences together into scaffolds in draft genome assemblies. Existing software for this purpose performs the scaffolding by joining sequences with a gap between them, not considering potential overlaps of contigs. We developed ARBitR to create scaffolds where overlaps are taken into account and show that it can accurately recreate regions where draft assemblies are broken. AVAILABILITY AND IMPLEMENTATION: ARBitR is written and implemented in Python3 for Unix-based operative systems. All source code is available at https://github.com/markhilt/ARBitR under the GNU General Public License v3. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Indexed as
Identifiers
What OpenQuestion holds
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.