Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

Equipment

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Analysis and compression of data from the third generation of sequencing instruments

2019/33/B/ST6/02040

Keywords:

genome sequencing data compression Oxford Nanopore Technology

Descriptors:

  • ST6_013:
  • ST6_006:
  • NZ2_007:

Panel:

ST6 - Computer science and informatics: informatics and information systems, computer science, scientific computing, intelligent systems

Host institution :

Politechnika Śląska, Wydział Automatyki, Elektroniki i Informatyki

woj. śląskie

Other projects carried out by the institution 

Principal investigator (from the host institution):

prof. Sebastian Tomasz Deorowicz 

Number of co-investigators in the project: 5

Call: OPUS 17 - announced on 2019-03-15

Amount awarded: 488 040 PLN

Project start date (Y-m-d): 2020-02-28

Project end date (Y-m-d): 2024-12-27

Project duration:: 58 months (the same as in the proposal)

Project status: Project settled

Project description

Download the project description in a pdf file

Note - project descriptions were prepared by the authors of the applications themselves and placed in the system in an unchanged form.

Information in the final report

  • Publication in academic press/journals (16)
  1. Illumina reads correction - evaluation and improvements
    Authors:
    Maciej Długosz, Sebastian Deorowicz
    Academic press:
    Scientific Reports (rok: 2023, tom: nd, strony: nd), Wydawca: Springer
    Status:
    Submitted
  2. AGC: compact representation of assembled genomes with fast queries and updates
    Authors:
    Sebastian Deorowicz, Agnieszka Danek. Heng Li
    Academic press:
    Bioinformatics (rok: 2023, tom: 39, strony: btad097), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btad097 - link to the publication
  3. CoLoRd: compressing long reads
    Authors:
    Marek Kokot, Adam Gudyś, Heng Li, Sebastian Deorowicz
    Academic press:
    Nature Methods (rok: 2022, tom: 19, strony: 441-444), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1038/s41592-022-01432-3 - link to the publication
  4. PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences
    Authors:
    Andrzej Zieleziński, Sebastian Deorowicz, Adam Gudyś
    Academic press:
    Bioinformatics (rok: 2022, tom: 38, strony: 1447-1449), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btab837 - link to the publication
  5. Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2
    Authors:
    Jamshed Khan, Marek Kokot, Sebastian Deorowicz, Rob Patro
    Academic press:
    Genome Biology (rok: 2022, tom: 23, strony: 190), Wydawca: BMC
    Status:
    Published
    DOI:
    10.1186/s13059-022-02743-6 - link to the publication
  6. PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences
    Authors:
    Andrzej Zieleziński, Sebastian Deorowicz, Adam Gudyś
    Academic press:
    Bioinformatics (rok: 2022, tom: 38, strony: 1447-1449), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btab837 - link to the publication
  7. Illumina reads correction - evaluation and improvements
    Authors:
    Maciej Długosz, Sebastian Deorowicz
    Academic press:
    Scientific Reports (rok: 2023, tom: nd, strony: nd), Wydawca: Springer
    Status:
    Submitted
  8. Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2
    Authors:
    Jamshed Khan, Marek Kokot, Sebastian Deorowicz, Rob Patro
    Academic press:
    Genome Biology (rok: 2022, tom: 23, strony: 190), Wydawca: BMC
    Status:
    Published
    DOI:
    10.1186/s13059-022-02743-6 - link to the publication
  9. The Kmer File Format: a standardized and compact disk representation of sets of k-mers
    Authors:
    Y. Dufresne, T. Lemane, P. Marijon, P. Peterlongo, A. Rahman, Marek Kokot, P. Medvedev, Sebastian Deorowicz, R. Chikhi
    Academic press:
    Bioinformatics (rok: 2022, tom: 38, strony: 4423-4425), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btac528 - link to the publication
  10. Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2
    Authors:
    Jamshed Khan, Marek Kokot, Sebastian Deorowicz, Rob Patro
    Academic press:
    Genome Biology
    Status:
    Submitted
  11. PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences
    Authors:
    Andrzej Zieleziński, Sebastian Deorowicz, Adam Gudyś
    Academic press:
    Bioinformatics (rok: 2022, tom: 38, strony: 1447-1449), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btab837 - link to the publication
  12. The Kmer File Format: a standardized and compact disk representation of sets of k-mers
    Authors:
    Y. Dufresne, T. Lemane, P. Marijon, P. Peterlongo, A. Rahman, Marek Kokot, P. Medvedev, Sebastian Deorowicz, R. Chikhi
    Academic press:
    Bioinformatics , Wydawca: Oxford University Press
    Status:
    Submitted
  13. The Kmer File Format: a standardized and compact disk representation of sets of k-mers
    Authors:
    Y. Dufresne, T. Lemane, P. Marijon, P. Peterlongo, A. Rahman, Marek Kokot, P. Medvedev, Sebastian Deorowicz, R. Chikhi
    Academic press:
    Bioinformatics (rok: 2022, tom: 38, strony: 4423-4425), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btac528 - link to the publication
  14. CoLoRd: compressing long reads
    Authors:
    Marek Kokot, Adam Gudyś, Heng Li, Sebastian Deorowicz
    Academic press:
    Nature Methods (rok: 2022, tom: 19, strony: 441-444), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1038/s41592-022-01432-3 - link to the publication
  15. AGC: compact representation of assembled genomes with fast queries and updates
    Authors:
    Sebastian Deorowicz, Agnieszka Danek. Heng Li
    Academic press:
    Bioinformatics (rok: 2023, tom: 39, strony: btad097), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btad097 - link to the publication
  16. CoLoRd: compressing long reads
    Authors:
    Marek Kokot, Adam Gudyś, Heng Li, Sebastian Deorowicz
    Academic press:
    Nature Methods (rok: 2022, ), Wydawca: Springer Nature
    Status:
    Accepted for publication
    DOI:
    10.1038/s41592-022-01432-3 - link to the publication

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