Human parainfluenza virus (HPIV) genome annotation

How to annotate HPIV sequences with VADR

HPIV VADR model libraries

Additional VADR documentation

References

---

How to annotate HPIV genomes with VADR

Steps for using VADR for HPIV annotation:

1. Download and install the latest version of VADR, following the instructions on this page. Alternatively, you can use the StaPH-B VADR 1.6.3-hav-flu2 docker image created by Curtis Kapsak (docker image names: staphb/vadr:1.6.3-hav-flu2 and staphb/vadr:latest), available on dockerhub and quay. A brief README for the docker image is here.

2. Clone the latest HPIV VADR model library from this repository (current release v1.0)
   git clone git@github.com:greninger-lab/vadr-models-hpiv.git
   or download the current release from here.
   Note the path to the directory name created plus the specific type subdirectory (e.g. /path/to/vadr-models-hpiv/hpiv2) as <hpiv-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 18000 <input-fasta-file> > <trimmed-fasta-file>

4. Run the v-annotate.pl program on an input trimmed fasta file with HPIV sequences using the recommended command below. <hpiv-key> must be hpiv1, hpiv2, hpiv3, or hpiv4 and associated with the correct --mdir type directory (e.g. --mkey hpiv3 --mdir /path/to/vadr-models-hpiv/hpiv3).

v-annotate.pl -r --mkey <hpiv-key> --mdir <hpiv-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

---

HPIV VADR model libraries

• The VADR model libraries for HPIV annotation include models for types HPIV1, HPIV2, HPIV3, and HPIV4 (subtypes a and b).

---

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 HPIV from Mpox virus annotation

---