High Performance Integration Pipeline for Viral and Epitope Sequences

Abstract

With the spread of COVID-19, sequencing laboratories started to share hundreds of sequences daily. However, the lack of a commonly agreed standard across deposition databases hindered the exploration and study of all the viral sequences collected worldwide in a practical and homogeneous way. During the first months of the pandemic, we developed an automatic procedure to collect, transform, and integrate viral sequences of SARS-CoV-2, MERS, SARS-CoV, Ebola, and Dengue from four major database institutions (NCBI, COG-UK, GISAID, and NMDC). This data pipeline allowed the creation of the data exploration interfaces VirusViz and EpiSurf, as well as ViruSurf, one of the largest databases of integrated viral sequences. Almost two years after the first release of the repository, the original pipeline underwent a thorough refinement process and became more efficient, scalable, and general (currently, it also includes epitopes from the IEDB). Thanks to these improvements, we constantly update and expand our integrated repository, encompassing about 9.1 million SARS-CoV-2 sequences at present (March 2022). This pipeline made it possible to design and develop fundamental resources for any researcher interested in understanding the biological mechanisms behind the viral infection. In addition, it plays a crucial role in many analytic and visualization tools, such as ViruSurf, EpiSurf, VirusViz, and VirusLab.

Bioinformatics and High-Performance Computing Methods for Deciphering and Fighting COVID-19—Editorial

“…In High Performance Integration Pipeline for Viral and Epitope Sequences [ 10 ], Tommaso Alfonsi, Pietro Pinoli and Arif Canakoglu presented an integrated pipeline to collect, transform, and integrate viral sequences of SARS-CoV-2, MERS, SARS-CoV, Ebola, and Dengue from four major database institutions (NCBI, COG-UK, GISAID, and NMDC). This pipeline allowed the development of VirusViz and EpiSurf, two data exploration interfaces, and of ViruSurf, one of the largest databases of viral sequences.…”

Challenges of Software Engineering in Computational Biology and Bioinformatics Scientific Software Projects

“…The integration of efficient methodologies for data processing and retrieval of large amounts of data within these tools is a major problem in computational biology and in bioinformatics [6,7]. Data integration will allow for better management and facilitate the system's ability to store and retrieve data in addition to interacting with outside sources within the same field [8].…”