VADR

Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation

VADR

VADR is a suite of tools for classifying and analyzing sequences homologous to a set of reference models of viral genomes or gene families. It has been mainly tested for analysis of Norovirus, Dengue, and SARS-CoV-2 virus sequences in preparation for submission to the GenBank database.

Parameters

  • FASTA consensus file: file

    Sequencing file you want to get viral annotations from in the VADR pipeline

  • Reference Genome: option or File

    Can be Sketch format .msh or FASTA file.

Returns

_images/vadr1.png

  1. Table format: Tab-separated annotation

    5 column feature table output for passing sequences

_images/vadrtbl.png

  1. sgm format: Tab-separated annotation

    per-model-segment tabular summary file

_images/vadrsgm.png

  1. sqa format: Tab-separated file

    per-sequence tabular annotation summary file

_images/vadrsq.png

All output files created in directory your directory containing your input FASTA file under vadr_output

Note

See more information `here <https://github.com/ncbi/vadr/wiki/Coronavirus-annotation#many-alertserrors-in-orf3a-orf6-orf7a-orf7b-orf8-and-orf10-do-not-cause-a-sequence-to-fail-1`_

  1. Output printed to screen saved in: my4.vadr.log

  2. List of executed commands saved in: my4.vadr.cmd

  3. List and description of all output files saved in: my4.vadr.filelist

  4. esl-seqstat -a output for input fasta file saved in: my4.vadr.seqstat

  5. 5 column feature table output for passing sequences saved in: my4.vadr.pass.tbl

  6. 5 column feature table output for failing sequences saved in: my4.vadr.fail.tbl

  7. list of passing sequences saved in: my4.vadr.pass.list

  8. list of failing sequences saved in: my4.vadr.fail.list

  9. list of alerts in the feature tables saved in: my4.vadr.alt.list

  10. fasta file with passing sequences saved in: my4.vadr.pass.fa

  11. fasta file with failing sequences saved in: my4.vadr.fail.fa

  12. per-sequence tabular annotation summary file saved in: my4.vadr.sqa

  13. per-sequence tabular classification summary file saved in: my4.vadr.sqc

  14. per-feature tabular summary file saved in: my4.vadr.ftr

  15. per-model-segment tabular summary file saved in: my4.vadr.sgm

  16. per-alert tabular summary file saved in: my4.vadr.alt

  17. alert count tabular summary file saved in: my4.vadr.alc

  18. per-model tabular summary file saved in: my4.vadr.mdl

  19. alignment doctoring tabular summary file saved in: my4.vadr.dcr

  20. ungapped seed alignment summary file (-s) saved in: my4.vadr.sda

  21. replaced stretches of Ns summary file (-r) saved in: my4.vadr.rpn