Evidence map›Paper›PMID 38905513›Full record

ReviewGenomics, proteomics & bioinformatics2024

The Bioinformatic Applications of Hi-C and Linked Reads.

Libo Jiang, Michael A Quail, Jack Fraser-Govil, Haipeng Wang, Xuequn Shi, Karen Oliver, Esther Mellado Gomez, Fengtang Yang, Zemin Ning

Abstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in Genomics, proteomics & bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. 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

9 authors.

Libo JiangSchool of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China.ORCID 0000-0003-4703-9220
Michael A QuailThe Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.ORCID 0000-0002-3861-0483
Jack Fraser-GovilThe Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.ORCID 0000-0002-6980-8484
Haipeng WangSchool of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China.ORCID 0000-0002-2366-7946
Xuequn ShiCollege of Food Science and Technology, Hainan University, Haikou 570228, China.ORCID 0000-0002-6495-241X
Karen OliverThe Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.ORCID 0009-0005-8329-2284
Esther Mellado GomezThe Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.ORCID 0009-0001-7168-1734
Fengtang YangSchool of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China.ORCID 0000-0002-3573-2354
Zemin NingThe Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.ORCID 0000-0003-4359-776X

Funding

Wellcome TrustWellcome Trust GRANT NO. WT206194
6 · The paper itself

Abstract

Long-range sequencing grants insight into additional genetic information beyond what can be accessed by both short reads and modern long-read technology. Several new sequencing technologies, such as "Hi-C" and "Linked Reads", produce long-range datasets for high-throughput and high-resolution genome analyses, which are rapidly advancing the field of genome assembly, genome scaffolding, and more comprehensive variant identification. In this review, we focused on five major long-range sequencing technologies: high-throughput chromosome conformation capture (Hi-C), 10X Genomics Linked Reads, haplotagging, transposase enzyme linked long-read sequencing (TELL-seq), and single- tube long fragment read (stLFR). We detailed the mechanisms and data products of the five platforms and their important applications, evaluated the quality of sequencing data from different platforms, and discussed the currently available bioinformatics tools. This work will benefit the selection of appropriate long-range technology for specific biological studies.

Indexed as

Computational BiologyGenomicsHigh-Throughput Nucleotide SequencingAnimalsHumansSequence Analysis, DNAGenome assemblyHi-CLinked ReadsLong-range NGS readsQuality assessment

Identifiers

PMID38905513
PMCPMC11580686

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.