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CORDIS - EU research results
CORDIS

Long-TREC: The Long-Reads Transcriptomics European Consortium. The next generation transcriptome biology revealed by single molecule sequencing technologies

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Interim report including links to a protocol repository (opens in new window)

Updated report on the state of library preparation, sequencing and mapping algorithm developments, including links to a protocol repository (i.e. protocols.io) and GitHub for code of novel mapping algorithms

Interim report on the state of algorithm developments in WP4 applied to use cases (opens in new window)

Updated progress report on the state of algorithm developments in WP4, including a list of links to GitHub repositories containing code

Initial report on the state of algorithm developments in WP5 (opens in new window)
Interim report on the state of algorithm developed in WP5 and pipelines comparison (opens in new window)

Updated progress report on the state of algorithm developments in WP5 and comparison of pipelines

Initial progress report on the state of algorithm developments in WP3 (opens in new window)

Progress report on the state of algorithm developments in WP3

Progress report on the state of library preparation, sequencing and mapping algorithm (opens in new window)

Progress report on the state of library preparation, sequencing, and mapping algorithm developments.

Interim report on the state of algorithm developed in WP3, including benchmarks (opens in new window)

Updated progress report on the state of algorithm developments in WP3, including a list of links to a GitHub repository containing code

Progress report on the state of algorithm developments in WP4 (opens in new window)
LongTREC website and social network profiles (opens in new window)

Publications

IsoTools 2.0: Software for Comprehensive Analysis of Long-read Transcriptome Sequencing Data (opens in new window)

Author(s): Yalan Bi, Tom Lukas Lankenau, Matthias Lienhard, Ralf Herwig
Published in: Journal of Molecular Biology, 2025, ISSN 0022-2836
Publisher: Elsevier BV
DOI: 10.1016/j.jmb.2025.169049

Icarust, a real-time simulator for Oxford Nanopore adaptive sampling (opens in new window)

Author(s): Rory Munro, Satrio Wibowo, Alexander Payne, Matthew Loose
Published in: Bioinformatics, Issue 40, 2024, ISSN 1367-4811
Publisher: Oxford University Press (OUP)
DOI: 10.1093/bioinformatics/btae141

Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of<i>SF3B1</i>mutations (opens in new window)

Author(s): Alicja Pacholewska, Matthias Lienhard, Mirko Brüggemann, Heike Hänel, Lorina Bilalli, Anja Königs, Felix Heß, Kerstin Becker, Karl Köhrer, Jesko Kaiser, Holger Gohlke, Norbert Gattermann, Michael Hallek, Carmen D. Herling, Julian König, Christina Grimm, Ralf Herwig, Kathi Zarnack, Michal R. Schweiger
Published in: Genome Research, Issue 34, 2024, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/GR.279327.124

Evidence-based unification of potato gene models with the UniTato collaborative genome browser (opens in new window)

Author(s): Maja Zagorščak, Jan Zrimec, Carissa Bleker, Nadja Nolte, Mojca Juteršek, Živa Ramšak, Kristina Gruden, Marko Petek
Published in: Frontiers in Plant Science, Issue 15, 2024, ISSN 1664-462X
Publisher: Frontiers Media SA
DOI: 10.3389/FPLS.2024.1352253

Toward the use of nanopore RNA sequencing technologies in the clinic: challenges and opportunities (opens in new window)

Author(s): Xanthi-Lida Katopodi, Oguzhan Begik, Eva Maria Novoa
Published in: Nucleic Acids Research, Issue 53, 2025, ISSN 0305-1048
Publisher: Oxford University Press (OUP)
DOI: 10.1093/NAR/GKAF128

Profiling the epigenome using long-read sequencing (opens in new window)

Author(s): Tianyuan Liu, Ana Conesa
Published in: Nature Genetics, Issue 57, 2025, ISSN 1061-4036
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41588-024-02038-5

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