Author: Niema Moshiri
Title: ViralMSA: Massively scalable reference-guided multiple sequence alignment of viral genomes Document date: 2020_4_21
ID: l9a7upui_9
Snippet: ViralMSA takes the following as input: (1) a FASTA file containing the viral genomes to align, (2) the GenBank accession number of the reference genome to use, and (3) the mapper to utilize (Minimap2 by default). ViralMSA will pull the reference genome from GenBank and generate an index using the selected mapper, both of which will be cached for future alignments of the same viral strain, and will then execute the mapping. ViralMSA will then proc.....
Document: ViralMSA takes the following as input: (1) a FASTA file containing the viral genomes to align, (2) the GenBank accession number of the reference genome to use, and (3) the mapper to utilize (Minimap2 by default). ViralMSA will pull the reference genome from GenBank and generate an index using the selected mapper, both of which will be cached for future alignments of the same viral strain, and will then execute the mapping. ViralMSA will then process the results and output a multiple sequence alignment in the FASTA format. For commonly-studied viruses (e.g. HIV, SARS-CoV-2), the user can simply provide the name of the virus instead of an accession number, and ViralMSA will automatically select what we believe would be an appropriate reference genome.
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