Watch is an experimental command to classify a stream of sequencing data. Index indexes many signatures using a Sequence Bloom Tree (SBT).Ĭategorize is an experimental command to categorize many signatures. Info shows version and software information. those output by lca classify.įinally, there are a number of utility and information commands: Lca compare_csv compares lineage spreadsheets, e.g. Lca rankinfo summarizes the content of a database. Lca index creates a database for use with LCA subcommands. Lca gather finds non-overlapping matches to a metagenome in an LCA database.
Lca summarize summarizes the content of a metagenome using an LCA database. Lca classify classifies many signatures against an LCA database. Information these are grouped under the sourmash lca There are also a number of commands that work with taxonomic Gather finds non-overlapping matches to a metagenome in a collection of signatures. Search finds matches to a query signature in a collection of signatures. Plot plots distance matrices created by compare. See the tutorial for aĬompare compares signatures and builds a distance matrix. There are five main subcommands: compute, compare, plot, To get a list of subcommands, run sourmash without any arguments. The sourmash command and its subcommands ¶
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