Compression, stdin

If no positional arguments (with paths to input query sequence data) provided to the run subcommand, then Nextclade CLI will attempt to read uncompressed FASTA data from standard input (stdin).

In Nextclade CLI, for any of the arguments for input files (they start with --input-) you can also use special file name “-” to read uncompressed data from standard input (stdin).

This should allow embedding into Unix-style pipelines.


xzcat *.fasta.xz | nextclade run -D <dataset> -o- | xz -9 compressed.fasta.zst

Nextclade CLI supports the following compression formats: gz, bz2, xz, zst. If an input file name ends with one of these extensions, Nextclade CLI will transparently decompress this file. For multiple positional arguments (input query sequences), different compression formats can be used.


nextclade run -D <dataset> input1.fasta.gz input1.fasta.xz -o aligned.fasta.zst