ArticlePLoS computational biology2019
Integrating Hi-C links with assembly graphs for chromosome-scale assembly.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 506 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
506 citing papers in PubMed.
- A Mid-Atlantic Brook Trout (Salvelinus fontinalis) genome to advance conservation and comparative genomics.G3 (Bethesda, Md.) · 2026Article
- Convergent evolutionary loss of chemosensory and blood-feeding pathways in non-blood-feeding mosquitoes.bioRxiv : the preprint server for biology · 2026Article
- Chromosome-scale assembly of wheat cultivar Sumai 3, a major germplasm source for Fusarium head blight resistance.The plant genome · 2026Article
- Four haplotype-resolved genome assemblies and a reference-free 66-haplotype pangenome graph for Cannabis sativa.Scientific data · 2026Article
- Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet.Cell genomics · 2026Article
- Haplotype-phased genomes of the barley leaf rust pathogen reveal evidence of repeat element expansion and somatic hybridization.G3 (Bethesda, Md.) · 2026Article
- Chromosome-level reference genome of a foundational California native legume, Acmispon strigosus.The Journal of heredity · 2026Article
- A chromosome-level genome assembly for the beach-spawning California grunion, Leuresthes tenuis.The Journal of heredity · 2026Article
- The genome assemblies of the Tui chub, Siphateles bicolor, and Arroyo chub, Gila orcuttii.The Journal of heredity · 2026Article
- A genome assembly of the North American golden eagle, Aquila chrysaetos canadensis.The Journal of heredity · 2026Article
- Genome assembly for the Sierra Nevada Parnassian (Parnassius behrii) and a brief review of butterfly genome sizes.The Journal of heredity · 2026Review
- De Novo Genome Assemblies of Four Rainbow Trout Genetic Lines Reveal Structural Variants in Pursuit of a Pangenome Reference.Molecular ecology resources · 2026Article
- Wild tomato genome assemblies reveal structural variants and repeat content act as recombination barriers.Nature communications · 2026Article
- Telomere-to-telomere genome assembly of Metarhizium acridum provides insights into Metarhizium genome evolution.BMC genomics · 2026Article
- A reference genome for cultured Drosophila ovarian somatic cells enables studies of transposon and piRNA biology.Genome biology · 2026Article
- Elevated retrocopy burden and sloth-specific expansions illuminate mammalian genome evolution.BMC biology · 2026Article
- A genome assembly of Greene's tuctoria, Tuctoria greenei, an amphibious endemic and endangered California vernal pool grass.The Journal of heredity · 2026Article
- A genome assembly of Douglas' meadowfoam, Limnanthes douglasii R. BR.The Journal of heredity · 2026Article
- Genome assemblies of two bumble bee species: Bombus sonorus and Bombus vosnesenskii.The Journal of heredity · 2026Article
- Genome assembly and annotation of a deep-diving pinniped, the northern elephant seal (Mirounga angustirostris).The Journal of heredity · 2026Article
446 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
Long-read sequencing and novel long-range assays have revolutionized de novo genome assembly by automating the reconstruction of reference-quality genomes. In particular, Hi-C sequencing is becoming an economical method for generating chromosome-scale scaffolds. Despite its increasing popularity, there are limited open-source tools available. Errors, particularly inversions and fusions across chromosomes, remain higher than alternate scaffolding technologies. We present a novel open-source Hi-C scaffolder that does not require an a priori estimate of chromosome number and minimizes errors by scaffolding with the assistance of an assembly graph. We demonstrate higher accuracy than the state-of-the-art methods across a variety of Hi-C library preparations and input assembly sizes. The Python and C++ code for our method is openly available at https://github.com/machinegun/SALSA.
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.