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Known issues

For version 1.1 and later, consensus FASTA files generated for each sample, virus, and reference sequence incorrectly contain soft-masked sequences instead of hard-masked sequences. To get hard-masked sequences, use {sample_name}.consensus_hard_masked_sequence.fa or convert lowercase nucleotides to "N".

For version 1.1 and later, consensus FASTA files generated for each sample, virus, and reference sequence incorrectly contain soft-masked sequences instead of hard-masked sequences. To get hard-masked sequences, use {sample_name}.consensus_hard_masked_sequence.fa or convert lowercase nucleotides to "N".