Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses.
The advent of Next Generation Sequencing (NGS) technologies has opened new possibilities for researchers. However, the more biology becomes a data-intensive field, the more biologists have to learn how to process and analyze NGS data with complex computational tools. Even with the availability of common pipeline specifications, it is often a time-consuming and cumbersome task for a bench scientist to install and configure the pipeline tools. We believe that a unified, desktop and biologist-friendly front end to NGS data analysis tools will substantially improve productivity in this field. Here we present NGS pipelines "Variant Calling with SAMtools", "Tuxedo Pipeline for RNA-seq Data Analysis" and "Cistrome Pipeline for ChIP-seq Data Analysis" integrated into the Unipro UGENE desktop toolkit. We describe the available UGENE infrastructure that helps researchers run these pipelines on different datasets, store and investigate the results and re-run the pipelines with the same parameters. These pipeline tools are included in the UGENE NGS package. Individual blocks of these pipelines are also available for expert users to create their own advanced workflows.
Unipro Center for Information Technologies , Novosibirsk , Russia.
Olga
O
Golosova
Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, NIH , Bethesda, MD , USA.
Ross
R
Henderson
Unipro Center for Information Technologies , Novosibirsk , Russia.
Yuriy
Y
Vaskin
Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, NIH , Bethesda, MD , USA.
Andrei
A
Gabrielian
Unipro Center for Information Technologies , Novosibirsk , Russia.
German
G
Grekhov
Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, NIH , Bethesda, MD , USA.
Vijayaraj
V
Nagarajan
Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, NIH , Bethesda, MD , USA.
Andrew J
AJ
Oler
Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, NIH , Bethesda, MD , USA.
Mariam
M
Quiñones
Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, NIH , Bethesda, MD , USA.
Darrell
D
Hurt
Unipro Center for Information Technologies , Novosibirsk , Russia.
Mikhail
M
Fursov
Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, NIH , Bethesda, MD , USA.
Yentram
Y
Huyen
Bioinformatics; ChIP-seq; Data analysis; Next-generation sequencing; RNA-seq; Variant calling