A BED-like tab-separated value (TSV) file with no header row, consisting of the following columns:
chrom: each sequence name as it appears in Custom Reference FASTA
chromStart: start position (always set to 0)
chromEnd: end position (sequence length)
genomeName: full name of the virus the sequence belongs to (e.g. Monkeypox virus clade II)
(optional) segmentName: how this sequence is labeled within the virus (e.g. Segment 4 (HA)). Set to 'Full' if the sequence is the full genome
This file affects how sequences are labeled in the output.
Sequence names must match those in Custom Reference FASTA. The same set of sequences must appear in both.
If there are multiple viruses, their names should be unique. For example, if there are multiple Influenza genomes, they should not be labeled with the same virus name in the 4th column.
If the Custom Reference FASTA includes sequences from multiple segments, it is recommended to provide this BED file. Otherwise, each segment will be treated independently and not all of them may be used as reference.