We have collaborated on the following publications
2023
1.
Budiš, J.; Krampl, W.; Kucharík, M.; Hekel, R.; Goga, A.; Sitarčík, J.; Lichvár, M.; Smol'ak, D.; Böhmer, M.; Baláž, A.; Ďuriš, F.; Gazdarica, J.; Šoltys, K.; Turňa, J.; Radvánszky, J.; Szemes, T.
SnakeLines: integrated set of computational pipelines for sequencing reads Journal Article
In: Journal of integrative bioinformatics, 20 (3), 2023, ISSN: 16134516.
Abstract | Links | BibTeX | Tags: Computational pipeline
@article{Budiš2023,
title = {SnakeLines: integrated set of computational pipelines for sequencing reads},
author = {J. Budiš and W. Krampl and M. Kucharík and R. Hekel and A. Goga and J. Sitarčík and M. Lichvár and D. Smol'ak and M. Böhmer and A. Baláž and F. Ďuriš and J. Gazdarica and K. Šoltys and J. Turňa and J. Radvánszky and T. Szemes},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85179214150&doi=10.1515%2fjib-2022-0059&partnerID=40&md5=d6176bc0c7158cc8f4a5ee6fd000bbca},
doi = {10.1515/jib-2022-0059},
issn = {16134516},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Journal of integrative bioinformatics},
volume = {20},
number = {3},
abstract = {With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilising sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on bioinformatics processing, which is often too demanding for clinicians and researchers without a computational background. Another problem represents the reproducibility of computational analyses across separated computational centres with inconsistent versions of installed libraries and bioinformatics tools. We propose an easily extensible set of computational pipelines, called SnakeLines, for processing sequencing reads; including mapping, assembly, variant calling, viral identification, transcriptomics, and metagenomics analysis. Individual steps of an analysis, along with methods and their parameters can be readily modified in a single configuration file. Provided pipelines are embedded in virtual environments that ensure isolation of required resources from the host operating system, rapid deployment, and reproducibility of analysis across different Unix-based platforms. SnakeLines is a powerful framework for the automation of bioinformatics analyses, with emphasis on a simple set-up, modifications, extensibility, and reproducibility. The framework is already routinely used in various research projects and their applications, especially in the Slovak national surveillance of SARS-CoV-2. © 2023 the author(s), published by De Gruyter, Berlin/Boston.},
keywords = {Computational pipeline},
pubstate = {published},
tppubtype = {article}
}
With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilising sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on bioinformatics processing, which is often too demanding for clinicians and researchers without a computational background. Another problem represents the reproducibility of computational analyses across separated computational centres with inconsistent versions of installed libraries and bioinformatics tools. We propose an easily extensible set of computational pipelines, called SnakeLines, for processing sequencing reads; including mapping, assembly, variant calling, viral identification, transcriptomics, and metagenomics analysis. Individual steps of an analysis, along with methods and their parameters can be readily modified in a single configuration file. Provided pipelines are embedded in virtual environments that ensure isolation of required resources from the host operating system, rapid deployment, and reproducibility of analysis across different Unix-based platforms. SnakeLines is a powerful framework for the automation of bioinformatics analyses, with emphasis on a simple set-up, modifications, extensibility, and reproducibility. The framework is already routinely used in various research projects and their applications, especially in the Slovak national surveillance of SARS-CoV-2. © 2023 the author(s), published by De Gruyter, Berlin/Boston.