Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

doc: since at least v2 we don't accept plain txt sequences #1257

Merged
merged 2 commits into from
Sep 20, 2023
Merged

doc: since at least v2 we don't accept plain txt sequences #1257

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
06b6ee9
doc: since at least v2 we don't accept plain txt sequences
corneliusroemer Sep 19, 2023
469b740
doc: reference requires fasta since v2, txt not accepted
corneliusroemer Sep 19, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions docs/user/input-files.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,13 +10,13 @@ Nextclade Web (simple and advanced modes): accepted in "Sequences" drag & drop b

Nextclade CLI and Nextalign CLI accept fasta inputs as one or multiple positional arguments. Accepts plain or compressed FASTA files. If a compressed fasta file is provided, it will be transparently decompressed. Supported compression formats: `gz`, `bz2`, `xz`, `zstd`. Decompressor is chosen based on file extension. If there's multiple input files, then different files can have different compression formats. If positional arguments provided, the plain fasta input is read from standard input (stdin).

Accepted formats: [FASTA](https://en.wikipedia.org/wiki/FASTA_format) or plain text (one sequence per line).
Accepted formats: [FASTA](https://en.wikipedia.org/wiki/FASTA_format)

## Reference (root) sequence

Viral nucleotide sequence which serves as a reference for alignment and the analysis. Mutations are called relative to the reference sequence. It is expected to be the root of the [reference tree](#reference-tree). The best results are obtained when the reference sequence is a well-known consensus genome, of a very high quality, preferably complete and unambiguous (spans entire genome and has no ambiguous nucleotides).

Accepted formats: [FASTA](https://en.wikipedia.org/wiki/FASTA_format) or plain text. The file is expected to contain only 1 sequence.
Accepted formats: [FASTA](https://en.wikipedia.org/wiki/FASTA_format) file containing exactly 1 sequence.

Nextclade Web (advanced mode): accepted in "Root sequence" drag & drop box. A remote URL is also accepted in `input-root-sequence` URL parameter.

Expand Down