diff --git a/doc/command-line.md b/doc/command-line.md index 3d6212c769..664998c8a7 100644 --- a/doc/command-line.md +++ b/doc/command-line.md @@ -137,6 +137,7 @@ The `sketch translate` command reads in **DNA sequences**, translates them in al The `sketch fromfile` command takes in a CSV file containing the locations of genomes and proteomes, and outputs all of the requested sketches. It is primarily intended for large-scale database construction. +(`fromfile` is a new command as of sourmash v4.4.0.) All of the `sourmash sketch` commands take FASTA or FASTQ sequences as input; input data can be uncompressed, compressed with gzip, or diff --git a/doc/sourmash-sketch.md b/doc/sourmash-sketch.md index 1dd380d76e..42a163d335 100644 --- a/doc/sourmash-sketch.md +++ b/doc/sourmash-sketch.md @@ -24,6 +24,7 @@ The `sketch translate` command reads in **DNA sequences**, translates them in al The `sketch fromfile` command takes in a CSV file containing the locations of genomes and proteomes, and outputs all of the requested sketches. It is primarily intended for large-scale database construction. +(`fromfile` is a new command as of sourmash v4.4.0.) All `sourmash sketch` commands take FASTA or FASTQ sequences as input; input data can be uncompressed, compressed with gzip, or compressed @@ -88,6 +89,8 @@ use `sketch protein` to build signatures. ### Bulk sketch construction from many files +(This was added as of sourmash v4.4.0.) + The `sourmash sketch fromfile` command is intended for use when building many signatures as part of a larger workflow. It supports a variety of options to build new signatures, parallelize @@ -108,7 +111,7 @@ can be empty for a given row; likewise, if no DNA sketches are requested, `genome_filename` can be empty for a given row. Some of the key command-line options supported by `fromfile` are: -* `-o/--output-signatures` will save generated signatures to any of the [standard supported output formats](command-line.md#saving-signatures-more-generally). +* `-o/--output-signatures` will save generated signatures to any of the [standard supported output formats](command-line.md#choosing-signature-output-formats). * `-o/--output-csv-info` will save a CSV file of input filenames and parameter strings for use with the `sourmash sketch` command line; this can be used to construct signatures in parallel. * `--already-done` will take a list of existing signatures/databases to check against; signatures with matching names and parameter strings will not be rebuilt. * `--output-manifest-matching` will output a manifest of already-existing signatures, which can then be used with `sourmash sig cat` to collate signatures across databases; see [using manifests](command-line.md#using-manifests-to-explicitly-refer-to-collections-of-files). (This provides [`sourmash sig check` functionality](command-line.md#sourmash-signature-check---compare-picklists-and-manifests) in `sketch fromfile`.)