genBaRcode: a comprehensive R-package for genetic barcode analysis

Publikation: Beitrag in FachzeitschriftForschungsartikelBeigetragenBegutachtung

Beitragende

Abstract

MOTIVATION: Genetic barcodes have been established as an efficient method to trace clonal progeny of uniquely labeled cells by introducing artificial genetic sequences into the corresponding genomes. The assessment of those sequences relies on next generation sequencing and the subsequent analysis aiming to identify sequences of interest and correctly quantifying their abundance.

RESULTS: We developed the genBaRcode package as a toolbox combining the flexibility of digesting next generation sequencing reads with or without a sophisticated barcode structure, with a variety of error-correction approaches and the availability of several types of visualization routines. Furthermore, a graphical user interface was incorporated to allow also less experienced R users package-based analyses. Finally, the provided tool is intended to bridge the gap between generating and analyzing barcode data and thereby supporting the establishment of standardized and reproducible analysis strategies.

AVAILABILITY AND IMPLEMENTATION: The genBaRcode package is available at CRAN (https://cran.r-project.org/package=genBaRcode).

Details

OriginalspracheEnglisch
Seiten (von - bis)2189-2194
Seitenumfang6
FachzeitschriftBioinformatics
Jahrgang36
Ausgabenummer7
PublikationsstatusVeröffentlicht - 1 Apr. 2020
Peer-Review-StatusJa

Externe IDs

Scopus 85083040934
ORCID /0000-0002-2524-1199/work/142251506
ORCID /0000-0002-5726-4491/work/153109652

Schlagworte

Schlagwörter

  • Electronic Data Processing, Genetic Testing, High-Throughput Nucleotide Sequencing, Software