VariantSeq
VariantSeq is a Client-Desktop Application of the GPRO suite that uses best practices for analysis of Single Nucleotide Polymorphisms (SNP) and indels from DNA and VariantSeq data using the State-of-the -Art protocols. Tools for analysis of CNVs and/or structural variants are not yet implemented in the protocol. The application is an interface-based solution coupled with an infrastructure of server side dependencies (pipelines, databases and tools) that we distribute in a docker container that can be installed on a remote server or on a PC with sufficient RAM. The application also includes a File Transfer Protocol system (FTP) to facilitate the upload and download of files from the user’s computer to or from the server; a progress tracker (job tracking system), and two different execution modes (a “step-by-step” mode, and a “pipeline-like” mode).
Citing us
If you want to cite VariantSeq:
Hafez, A. I., Soriano, B., Elsayed, A. A., Futami, R., Ceprian, R., Ramos-Ruiz, R., Martinez, G., Roig, F. J., Torres-Font, M. A., Naya-Catala, F., Calduch-Giner, J. A., Trilla-Fuertes, L., Gamez-Pozo, A., Arnau, V., Sempere-Luna, J. M., Perez-Sanchez, J., Gabaldon, T., & Llorens, C. (2023). Client Applications and Server-Side Docker for Management of RNASeq and/or VariantSeq Workflows and Pipelines of the GPRO Suite. Genes, 14(2), 267. https://doi.org/10.3390/genes14020267
If you want to cite GPRO Suite Project:
Futami R, Muñoz-Pomer A, Viu JM, Dominguez-Escribá L, Covelli L, Bernet GP, Sempere JM, Moya A, Llorens C. GPRO: the professional tool for management, functional analysis and annotation of omic sequences and databases (2011). Biotechvana Bioinformatics: 2011-SOFT3
