DFAST_VRL

SARS-CoV-2 genome annotation and data submission tool to DDBJ

DFAST_VRL consists of NCBI VADR and associated scripts to facilitate data submission to DDBJ.
Source code is available at Github: nigyta/dfast_vrl

If you want to try the pipeline, use sample files available from here: Assembled contig file (FASTA), Metadata txt file

Only 1 genome per FASTA file is acceptable. (Complete genome in a single-FASTA file or draft genome in a multi-FASTA file)

Optional, but it is recommended to specify a unique value to distinguish the sample. For DDBJ submission, specify an isolate name like 'SARS-CoV-2/host/location/isolate/date'.

When enabled, query FASTA will be modified based on the mapping result to the reference. (Will extract mapped regions and discard unmapped. If the mapped regions are fragmented, they will be scaffolded (concatenated) using runs of Ns representing assembly gaps of estimated length.)

Disable scaffolding process. Ignored when 'Modify query FASTA' is not specified.