message: docs: prettify faq
diff: -# General
  -## What does nextclade do? What do I need to know?
  +# Frequently asked questions
  +
  +## General
  +
  +### What does nextclade do? What do I need to know?
  +
  Nextclade allows you to analyze SARS-CoV-2 sequences in the web browser. It will align your sequence data to a reference genome, call mutations relative to that reference, and place your sequences on a SARS-CoV-2 phylogeny. It also reports clade assignments and quality of your sequence data.
  -## Does my sequence data leave my computer?
  +### Does my sequence data leave my computer?
  +
  No, it does not. All steps - sequence alignment, variant calling, clade assignment, and tree placement - is happening on your computer, in your browser.
  -## What do the QC indicators mean?
  +
  +### What do the QC indicators mean?
  +
  Nextclade calculates several metrics that indicate sequence quality. We currently use four such metrics:
  - **Missing data**: the number of unknown bases (`N`)
  - **Mixed sites**: the number of bases that are not `ACTG-N`, for example `R`,`Y`,`K` etc.
  @@ -14,23 +21,15 @@ Nextclade calculates several metrics that indicate sequence quality. We currentl
  The rules on missing data, private mutations, and SNP clusters mimic the exclusion criteria used by the nextstrain augur tool.
  -## How can I contact the creators of Nextclade?
  -The nextstrain team maintains a discussion forum at discussion.nextstrain.org. You can post your questions there. For bugs in the software or feature requests, please open an issue on [GitHub](https://github.com/nextstrain/nextclade/issues).
  +### How can I contact the maintainers of Nextclade?
  -## Can I use my own tree?
  -Yes, you can specify your own tree, reference sequence, and QC settings in the advanced mode. Your phylogenetic tree can be generated using the augur pipeline.
  +The Nextstrain team maintains a discussion forum at https://discussion.nextstrain.org. You can post your questions there. For software bugs, feature requests, ideas, technical questions please open an issue on [GitHub](https://github.com/nextstrain/nextclade/issues/new/choose) (requires account registration).
  -## Is Nextclade available for other pathogens and microorganisms, too?
  -Nextclade works for other viruses, but you have to specify your own reference sequences, trees, and annotations. Only SARS-CoV-2 data is currently provided as a default. We plan to support other pathogens in the future.
  -
  -
  -# Output files
  +### Can I use my own reference tree?
  -## CSV/TSV outputs
  +Yes, you can specify your own tree, reference sequence, QC configuration and other parameters in the advanced mode. Your phylogenetic tree can be generated using the augur ([docs](https://docs.nextstrain.org/), [GitHub](https://github.com/nextstrain/augur)).
  -## JSON output
  -
  -
  -## Auspice tree output
  +### Is Nextclade available for other pathogens and microorganisms, too?
  +Nextclade works for other viruses, but you have to specify your own reference sequences, trees, and annotations. Only SARS-CoV-2 data is currently provided as a default. We plan to support other pathogens in the future.
  