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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Compression and analysis of genomic data

2015/17/B/ST6/01890

Keywords:

data compression genomics compressed data structures external algorithms

Descriptors:

  • ST6_6: Algorithms, parallel, distributed and network algorithms, algorithmic game theory
  • ST6_13: Bioinformatics, biocomputing, DNA and molecular computation
  • NZ2_7: Bioinformatics

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):

dr hab. Sebastian Deorowicz 

Number of co-investigators in the project: 8

Call: OPUS 9 - announced on 2015-03-16

Amount awarded: 539 920 PLN

Project start date (Y-m-d): 2016-03-01

Project end date (Y-m-d): 2019-10-31

Project duration:: 44 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.

Equipment purchased [PL]

  1. Przenośne stacje robocze (2 szt.) (28 000 PLN)
  2. Stacjonarna stacja robocza (11 300 PLN)

Information in the final report

  • Publication in academic press/journals (8)
  • Articles in post-conference publications (2)
  1. FQSqueezer: k-mer-based compression of sequencing data
    Authors:
    Sebastian Deorowicz
    Academic press:
    Bioinformatics (rok: 2019, tom: brak, strony: brak), Wydawca: Oxford University Press
    Status:
    Submitted
    DOI:
    brak - link to the publication
  2. Whisper 2: indel-sensitive short read mapping
    Authors:
    Sebastian Deorowicz, Adam Gudyś
    Academic press:
    Bioinformatics , Wydawca: Oxford Uiversity Press
    Status:
    Submitted
    DOI:
    brak - link to the publication
  3. Kmer-db: instant evolutionary distance estimation
    Authors:
    Sebastian Deorowicz, Adam Gudyś, Maciej Długosz, Marek Kokot, Agnieszka Danek
    Academic press:
    Bioinformatics (rok: 2019, tom: 35, strony: 133-136), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/bty610 - link to the publication
  4. CoMSA: compression of protein multiple sequence alignment files
    Authors:
    Sebastian Deorowicz, Joanna Walczyszyn, Agnieszka Debudaj-Grabysz
    Academic press:
    Bioinformatics (rok: 2019, tom: 35, strony: 227-234), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/bty619 - link to the publication
  5. FAMSA: Fast and accurate multiple sequence alignment of huge protein families
    Authors:
    Sebastian Deorowicz, Agnieszka Debudaj-Grabysz & Adam Gudyś
    Academic press:
    Scientific Reports (rok: 2016, tom: 6, strony: Article no. 33964), Wydawca: Nature Publishing Group
    Status:
    Published
    DOI:
    10.1038/srep33964 - link to the publication
  6. GTC: how to maintain huge genotype collections in a compressed form
    Authors:
    Agnieszka Danek, Sebastian Deorowicz
    Academic press:
    Bioinformatics (rok: 2018, tom: 34, strony: 1834-1840), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/bty023 - link to the publication
  7. KMC 3: counting and manipulating k -mer statistics
    Authors:
    Marek Kokot, Maciej Długosz, Sebastian Deorowicz
    Academic press:
    Bioinformatics (rok: 2017, tom: 33, strony: 2759-2761), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btx304 - link to the publication
  8. Whisper: Read sorting allows robust mapping of sequencing data
    Authors:
    Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Adam Gudyś, Szymon Grabowski
    Academic press:
    Bioinformatics (rok: 2019, tom: 35, strony: 2043-2050), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/bty927 - link to the publication
  1. Improvements in DNA Reads Correction
    Authors:
    Maciej Długosz, Sebastian Deorowicz, and Marek Kokot
    Conference:
    International Conference on Man-Machine Interactions (rok: 2017, ), Wydawca: Springer
    Data:
    konferencja October 3-6, 2017
    Status:
    Published
  2. Even faster sorting of (not only) integers
    Authors:
    Marek Kokot, Sebastian Deorowicz, and Maciej D lugosz
    Conference:
    International Conference on Man-Machine Interactions (rok: 2017, ), Wydawca: Springer
    Data:
    konferencja October 3-6, 2017
    Status:
    Published

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