Human rhinovirus genome annotation

How to annotate HRV sequences with VADR

HRV VADR model libraries

Additional VADR documentation

References

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How to annotate HRV genomes with VADR

Steps for using VADR for HRV annotation:

1. Download and install the latest version of VADR, following the instructions on this page. Alternatively, you can use the StaPH-B VADR 1.6.4 docker image created by Curtis Kapsak (docker image names: staphb/vadr:1.6.4 and staphb/vadr:latest), available on dockerhub and quay. A brief README for the docker image is here.

2. Clone the latest HRV VADR model library from this repository. git clone git@github.com:greninger-lab/vadr-models-hrv.git
   

   Note the path to the directory name created plus the "hrvA", "hrvB" or "hrvC" subdirectory (e.g. /path/to/vadr-models-hrv/hrvA) as <hrv-models-dir-path> for step 4.

3. Remove terminal ambiguous nucleotides from your input fasta sequence file using the fasta-trim-terminal-ambigs.pl script in $VADRSCRIPTSDIR/miniscripts/.

   To remove terminal ambiguous nucleotides from your sequence file <input-fasta-file> and to remove short and long sequences to create a new trimmed file <trimmed-fasta-file>, execute:

$VADRSCRIPTSDIR/miniscripts/fasta-trim-terminal-ambigs.pl --minlen 50 --maxlen 8000 <input-fasta-file> > <trimmed-fasta-file>

4. Run the v-annotate.pl program on an input trimmed fasta file with HRV sequences using the recommended command below. In addition, you must indicate the HRV species hrvA, hrvB or hrvC as <hrv-key>.

   For hrvA, run:

v-annotate.pl -r --r_file <hrv-models-dir-path>/hrvA.rpn.fa --mkey <hrv-key> --mdir <hrv-models-dir-path> <fasta-file-to-annotate> <output-directory-to-create>

For hrvB or hrvC, run:

v-annotate.pl -r --mkey <hrv-key> --mdir <hrv-models-dir-path> <fasta-file-to-annotate> <output-directory-to-create>

5. After running the v-annotate.pl command in step 4, there will be a number of files generated in the <output-directory-to-create>. Among these files, there are 5-column tab-delimited feature table files that end with the suffix .tbl. There is a separate file for passing (XXXXX.vadr.pass.tbl) and failing (XXXXX.vadr.fail.tbl) sequences. The format of the .tbl files is described here: https://www.ncbi.nlm.nih.gov/genbank/feature_table/

   More information about understanding failures and error alerts can be found in the VADR documentation here: https://github.com/ncbi/vadr/blob/master/documentation/annotate.md

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HRV VADR model library

• The VADR model libraries for HRV annotation were developed using representative RefSeq sequences NC_001617(A), NC_001490(B) and NC_009996(C).​

• All 3 of the model genomes have been modified slightly on the 3' end to have polyA tails of consistent length and facilitate consistent behavior across the models.

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Additional VADR documentation

• VADR README
• VADR installation instructions
  • Installation using vadr-install.sh
  • Setting environment variables
  • Verifying successful installation
  • Further information
• v-build.pl example usage and command-line options
  • v-build.pl example usage
  • v-build.pl command-line options
  • Building a VADR model library
  • How the VADR 1.0 model library was constructed
• v-annotate.pl example usage, command-line options and alert information
  • v-annotate.pl example usage
  • v-annotate.pl command-line options
  • Basic Information on v-annotate.pl alerts
  • Additional information on v-annotate.pl alerts
• Explanations and examples of v-annotate.pl detailed alert and error messages
  • Output fields with detailed alert and error messages
  • Explanation of sequence and model coordinate fields in .alt files
  • toy50 toy model used in examples of alert messages
  • Examples of different alert types and corresponding .alt output
  • Posterior probability annotation in VADR output Stockholm alignments
• VADR output file formats
  • VADR output files created by all VADR scripts
  • v-build.pl output files
  • v-annotate.pl output files
  • VADR coords coordinate string format
  • VADR sequence naming conventions

Reference

• The recommended citation for using VADR is: Alejandro A Schäffer, Eneida L Hatcher, Linda Yankie, Lara Shonkwiler, J Rodney Brister, Ilene Karsch-Mizrachi, Eric P Nawrocki; VADR: validation and annotation of virus sequence submissions to GenBank. BMC Bioinformatics 21, 211 (2020). https://doi.org/10.1186/s12859-020-3537-3

• This page was adapted for HRV from Mpox virus annotation

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