ArticleGenome biology2015
ALLMAPS: robust scaffold ordering based on multiple maps.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 235 papers.
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Who cites it
235 citing papers in PubMed.
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- Structural Variation and 3D Genome-Driven DNA/RNA Methylation Divergence Contributing to Cotton Fiber Domestication.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
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- High-resolution genome and genetic map of tetraploid Allium porrum expose pericentromeric recombination.The plant genome · 2025Article
- The pomegranate (Punica granatum L. cv. 'Wonderful') genome and P. protopunica shed light on pomegranate domestication. Is Daru a wild stock?BMC genomics · 2025Article
- The Evolution of Locally Adaptive Chromosome Inversions in Mimulus guttatus.Molecular ecology · 2025Article
- JG2: an updated version of the Japanese population-specific reference genome.Human genome variation · 2025Article
- Duckweed Evolution: from Land back to Water.Genomics, proteomics & bioinformatics · 2025Article
- The first complete assembly for a lungless urodelan with a "miniaturized" genome, the Northern Dusky Salamander (Plethodontidae: Desmognathus fuscus).G3 (Bethesda, Md.) · 2025Article
- Chromosome-level haplotype-resolved genome assembly provides insights into the highly heterozygous genome of Italian ryegrass (Lolium multiflorum Lam.).The plant genome · 2025Article
- Phased chromosome-level assembly provides insight into the genome architecture of hexaploid sweetpotato.Nature plants · 2025Article
175 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ordering and orientation of genomic scaffolds to reconstruct chromosomes is an essential step during de novo genome assembly. Because this process utilizes various mapping techniques that each provides an independent line of evidence, a combination of multiple maps can improve the accuracy of the resulting chromosomal assemblies. We present ALLMAPS, a method capable of computing a scaffold ordering that maximizes colinearity across a collection of maps. ALLMAPS is robust against common mapping errors, and generates sequences that are maximally concordant with the input maps. ALLMAPS is a useful tool in building high-quality genome assemblies. ALLMAPS is available at: https://github.com/tanghaibao/jcvi/wiki/ALLMAPS .
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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.