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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Memory efficient algorithms for processing and analysis of genome sequencing data

2012/05/B/ST6/03148

Keywords:

genome analysis sequencing external algorithms data compression

Descriptors:

  • NZ2_7: Bioinformatics
  • NZ2_8: Computational biology
  • ST6_6: Algorithms, parallel, distributed and network algorithms, algorithmic game theory

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: 6

Call: OPUS 3 - announced on 2012-03-15

Amount awarded: 463 000 PLN

Project start date (Y-m-d): 2013-02-15

Project end date (Y-m-d): 2017-02-14

Project duration:: 48 months (the same as in the proposal)

Project status: Project settled

Equipment purchased [PL]

  1. Wydajne przenośne stacje robocze.
  2. Wydajna stacja robocza (28 000 PLN)

Information in the final report

  • Publication in academic press/journals (7)
  • Articles in post-conference publications (2)
  1. Data compression for sequencing data
    Authors:
    Sebastian Deorowicz, Szymon Grabowski
    Academic press:
    Algorithms for Molecular Biology (rok: 2013, tom: 8, strony: 45304), Wydawca: BioMed Central
    Status:
    Published
    DOI:
    10.1186/1748-7188-8-25 - link to the publication
  2. CoMeta: Classification of metagenomes using k-mers
    Authors:
    Jolanta Kawulok, Sebastian Deorowicz
    Academic press:
    PLOS ONE (rok: 2015, tom: 10, strony: e0121453: 1-23), Wydawca: PLOS
    Status:
    Published
    DOI:
    10.1371/journal.pone.0121453 - link to the publication
  3. Disk-based compression of data from genome sequencing
    Authors:
    Szymon Grabowski, Sebastian Deorowicz, Łukasz Roguski
    Academic press:
    Bioinformatics (rok: 2015, tom: 31, strony: 1389-1395), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btu844 - link to the publication
  4. Indexing arbitrary-length k-mers in sequencing reads
    Authors:
    Tomasz Kowalski, Szymon Grabowski, Sebastian Deorowicz
    Academic press:
    PLOS One (rok: 2015, tom: 10, strony: e0133198), Wydawca: PLOS
    Status:
    Published
    DOI:
    10.1371/journal.pone.0133198 - link to the publication
  5. RECKONER: Read Error Corrector Based on KMC
    Authors:
    Maciej Długosz, Sebastian Deorowicz
    Academic press:
    Bioinformatics (rok: 2017, tom: 33, strony: 1086-1089), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btw746 - link to the publication
  6. DSRC 2—Industry-oriented compression of FASTQ files
    Authors:
    Łukasz Roguski, Sebastian Deorowicz
    Academic press:
    Bioinformatics (rok: 2014, tom: 30, strony: 2213-2215), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btu208 - link to the publication
  7. KMC 2: fast and resource-frugal k-mer counting
    Authors:
    Sebastian Deorowicz, Marek Kokot, Szymon Grabowski, Agnieszka Debudaj-Grabysz
    Academic press:
    Bioinformatics (rok: 2015, tom: 31, strony: 1569-1576), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btv022 - link to the publication
  1. Robust mapping of whole genome sequencing data
    Authors:
    S. Deorowicz, A. Debudaj-Grabysz, Sz. Grabowski, A. Gudyś
    Conference:
    The Biology of Genomes (rok: 2017, ), Wydawca: Cold Spring Harbor Laboratory
    Data:
    konferencja 9-13 maja
    Status:
    Submitted
  2. An Improved Algorithm for Fast and Accurate Classification of Sequences
    Authors:
    Jolanta Kawulok, Sebastian Deorowicz
    Conference:
    Beyond Databases, Architectures, and Structures (rok: 2014, ), Wydawca: Springer
    Data:
    konferencja 27-30 maja 2014
    Status:
    Published

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