ASPICov

ASPICov identifies nucleotide variants in SARS-CoV-2 genomes from Next Generation Sequencing (NGS) data, supporting analysis of capture and amplicon workflows on Illumina and Ion Torrent platforms.

Key Features:

• Broad Application Scope: Supports samples generated by capture and amplicon strategies and NGS data from Illumina and Ion Torrent technologies.
• Rapid and Reliable Analysis: Processes NGS data to identify nucleotide variants with an emphasis on speed and accuracy.
• FAIR Data Compliance: Implements nf-core guidelines aligned with FAIR principles (Findable, Accessible, Interoperable, Reusable) to promote transparency and reproducibility.
• Containerization with Singularity: Uses Singularity containers to provide a consistent computational environment across systems.
• Nextflow Implementation: Implemented in Nextflow to enable scalable and reproducible workflow management.

Scientific Applications:

• Epidemiological Studies: Identification of SARS-CoV-2 variants to track viral spread and evolution.
• Public Health Surveillance: Genomic surveillance of variant prevalence and geographic distribution.
• Vaccine Development: Analysis of genetic variation relevant to assessing vaccine efficacy against emerging strains.
• Antiviral Drug Research: Detection of mutations that may inform development of targeted antiviral therapies.

Methodology:

Processes sequencing reads, aligns them to reference genomes, and identifies nucleotide variants; implemented in Nextflow, packaged with Singularity, and following nf-core guidelines.