COVID-Align

COVID-Align aligns hCoV-19 (SARS-CoV-2) genomes using a profile hidden Markov model to produce rapid, accurate multiple-sequence alignments for comparative genomics and surveillance analyses.

Key Features:

• Profile HMM (HMMER): Uses a profile hidden Markov model estimated with HMMER tailored to hCoV-19 genomes, leveraging their conserved nature with minimal indels and no recombination events.
• Core reference alignment: Aligns new genomes to an existing core alignment derived from a dataset of approximately 2,500 high-quality hCoV-19 genomes.
• Efficiency: Processes large datasets, demonstrated by aligning 1,000 genomes in under 20 minutes on a computational cluster.
• Quality assessment and evolutionary analysis: Produces summary statistics to assess sequencing quality, identifies new mutations and indels, and flags sequences with sequencing or assembly errors.

Scientific Applications:

• Genomic surveillance: Enables rapid alignment of newly sequenced hCoV-19 genomes to support monitoring of viral evolution and transmission patterns.
• Quality control: Filters or flags problematic sequences with sequencing or assembly errors to improve downstream analyses.
• Comparative genomics and diversity studies: Facilitates comparison of new genomes against a core set of well-characterized sequences to study genetic diversity and novel variants.

Methodology:

A profile HMM was estimated with HMMER from a core dataset of approximately 2,500 high-quality hCoV-19 genomes and integrated into COVID-Align to align new sequences to the core alignment.