SnakeLines: integrated set of computational pipelines for sequencing reads
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.
- Location
-
Deutsche Nationalbibliothek Frankfurt am Main
- Extent
-
Online-Ressource
- Language
-
Englisch
- Bibliographic citation
-
SnakeLines: integrated set of computational pipelines for sequencing reads ; volume:20 ; number:3 ; year:2023 ; extent:12
Journal of integrative bioinformatics ; 20, Heft 3 (2023) (gesamt 12)
- Creator
-
Budiš, Jaroslav
Krampl, Werner
Kucharík, Marcel
Hekel, Rastislav
Goga, Adrián
Sitarčík, Jozef
Lichvár, Michal
Smol’ak, Dávid
Böhmer, Miroslav
Baláž, Andrej
Ďuriš, František
Gazdarica, Juraj
Šoltys, Katarína
Turňa, Ján
Radvánszky, Ján
Szemes, Tomáš
- DOI
-
10.1515/jib-2022-0059
- URN
-
urn:nbn:de:101:1-2023123013034709838836
- Rights
-
Open Access; Der Zugriff auf das Objekt ist unbeschränkt möglich.
- Last update
-
15.08.2025, 7:34 AM CEST
Data provider
Deutsche Nationalbibliothek. If you have any questions about the object, please contact the data provider.
Associated
- Budiš, Jaroslav
- Krampl, Werner
- Kucharík, Marcel
- Hekel, Rastislav
- Goga, Adrián
- Sitarčík, Jozef
- Lichvár, Michal
- Smol’ak, Dávid
- Böhmer, Miroslav
- Baláž, Andrej
- Ďuriš, František
- Gazdarica, Juraj
- Šoltys, Katarína
- Turňa, Ján
- Radvánszky, Ján
- Szemes, Tomáš
Other Objects (12)
Targeted sequencing analysis pipeline for species identification of human pathogenic fungi using long-read nanopore sequencing
ProcaryaSV: structural variation detection pipeline for bacterial genomes using short-read sequencing
iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites
From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy
TreeToReads - a pipeline for simulating raw reads from phylogenies
DNA read count calibration for single-molecule, long-read sequencing
Long-read sequencing in human genetics
Gene prediction in metagenomic sequencing reads
NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data
SNAKE
SNAKE
SNAKE
Targeted sequencing analysis pipeline for species identification of human pathogenic fungi using long-read nanopore sequencing
ProcaryaSV: structural variation detection pipeline for bacterial genomes using short-read sequencing
iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites
From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy
TreeToReads - a pipeline for simulating raw reads from phylogenies
DNA read count calibration for single-molecule, long-read sequencing
Long-read sequencing in human genetics
Gene prediction in metagenomic sequencing reads
NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data
SNAKE
SNAKE
SNAKE
Targeted sequencing analysis pipeline for species identification of human pathogenic fungi using long-read nanopore sequencing
ProcaryaSV: structural variation detection pipeline for bacterial genomes using short-read sequencing
iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites
From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy
TreeToReads - a pipeline for simulating raw reads from phylogenies
DNA read count calibration for single-molecule, long-read sequencing
Long-read sequencing in human genetics
Gene prediction in metagenomic sequencing reads
NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data
SNAKE
SNAKE