Submitters can specify reference sequences by the following two ways.

  • When accessioned reference is in the repository, specify by the INSDC/RefSeq accession.version.
  • When not in the repository, specify by uploading multi-fasta.

For the unmapped bam from PacBio and IonTorrent, neither the mapping table nor reference multi-fasta are not necessary.

For details, please see the manual.