Evidence map›Paper›PMID 39008464›Full record

ArticlePloS one2024

Puzzle Hi-C: An accurate scaffolding software.

Guoliang Lin, Zhiru Huang, Tingsong Yue, Jing Chai, Yan Li, Huimin Yang, Wanting Qin, Guobing Yang, Robert W Murphy, Ya-Ping Zhang and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in PloS one, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors.

Guoliang LinState Key Laboratory for Conservation and Utilization of Bio-resource, School of Ecology and Environment, School of Life Sciences and School of Medicine, Yunnan University, Kunming, Yunnan, China.
Zhiru HuangDepartment of Biology, University of Waterloo, Waterloo, ON, Canada.
Tingsong YueState Key Laboratory for Conservation and Utilization of Bio-resource, School of Ecology and Environment, School of Life Sciences and School of Medicine, Yunnan University, Kunming, Yunnan, China.
Jing ChaiState Key Laboratory for Conservation and Utilization of Bio-resource, School of Ecology and Environment, School of Life Sciences and School of Medicine, Yunnan University, Kunming, Yunnan, China.
Yan LiState Key Laboratory for Conservation and Utilization of Bio-resource, School of Ecology and Environment, School of Life Sciences and School of Medicine, Yunnan University, Kunming, Yunnan, China.
Huimin YangState Key Laboratory for Conservation and Utilization of Bio-resource, School of Ecology and Environment, School of Life Sciences and School of Medicine, Yunnan University, Kunming, Yunnan, China.
Wanting QinState Key Laboratory for Conservation and Utilization of Bio-resource, School of Ecology and Environment, School of Life Sciences and School of Medicine, Yunnan University, Kunming, Yunnan, China.
Guobing YangState Key Laboratory for Conservation and Utilization of Bio-resource, School of Ecology and Environment, School of Life Sciences and School of Medicine, Yunnan University, Kunming, Yunnan, China.
Robert W MurphyReptilia Zoo and Education Centre, Vaughan, ON, Canada.
Ya-Ping ZhangState Key Laboratory for Conservation and Utilization of Bio-resource, School of Ecology and Environment, School of Life Sciences and School of Medicine, Yunnan University, Kunming, Yunnan, China.
Zijie ZhangState Key Laboratory for Conservation and Utilization of Bio-resource, School of Ecology and Environment, School of Life Sciences and School of Medicine, Yunnan University, Kunming, Yunnan, China.
Wei ZhouNational Pilot School of Software, Yunnan University, Kunming, Yunnan, China.
Jing LuoState Key Laboratory for Conservation and Utilization of Bio-resource, School of Ecology and Environment, School of Life Sciences and School of Medicine, Yunnan University, Kunming, Yunnan, China.ORCID 0000-0001-9349-8538

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

High-quality, chromosome-scale genomes are essential for genomic analyses. Analyses, including 3D genomics, epigenetics, and comparative genomics rely on a high-quality genome assembly, which is often accomplished with the assistance of Hi-C data. Curation of genomes reveal that current Hi-C-assisted scaffolding algorithms either generate ordering and orientation errors or fail to assemble high-quality chromosome-level scaffolds. Here, we offer the software Puzzle Hi-C, which uses Hi-C reads to accurately assign contigs or scaffolds to chromosomes. Puzzle Hi-C uses the triangle region instead of the square region to count interactions in a Hi-C heatmap. This strategy dramatically diminishes scaffolding interference caused by long-range interactions. This software also introduces a dynamic, triangle window strategy during assembly. Initially small, the window expands with interactions to produce more effective clustering. Puzzle Hi-C outperforms available scaffolding tools.

Indexed as

AlgorithmsGenomicsSoftwareChromosomesGenomeHumans

Identifiers

PMID39008464
PMCPMC11249255

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.