From b10b49050f9e9b215ff9f710e184597d1760c784 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 18 Feb 2018 09:37:15 -0800 Subject: [PATCH] address @taylorreiter comments --- doc/classifying-signatures.md | 17 ++++++++--------- doc/command-line.md | 4 ++-- 2 files changed, 10 insertions(+), 11 deletions(-) diff --git a/doc/classifying-signatures.md b/doc/classifying-signatures.md index e1702a825b..63b92dfed9 100644 --- a/doc/classifying-signatures.md +++ b/doc/classifying-signatures.md @@ -41,15 +41,14 @@ question to ask is the reverse: **what genomes are in my metagenome?** We have implemented two algorithms in sourmash to do this. -One, approaches based on lowest common ancestor ("LCA"), uses -taxonomic information from e.g. GenBank to classify individual k-mers, -and then infers taxonomic distributions of metagenome contents from -the presence of these individual k-mers. (This is the approach -pioneered by [Kraken](https://ccb.jhu.edu/software/kraken/) and many -other tools.) `sourmash lca` can be used to classify individual -genome bins with `classify`, or summarize metagenome taxonomy with -`summarize`. The [sourmash lca -tutorial](http://sourmash.readthedocs.io/en/latest/tutorials-lca.html) +One algorithm uses taxonomic information from e.g. GenBank to classify +individual k-mers, and then infers taxonomic distributions of +metagenome contents from the presence of these individual +k-mers. (This is the approach pioneered by +[Kraken](https://ccb.jhu.edu/software/kraken/) and many other tools.) +`sourmash lca` can be used to classify individual genome bins with +`classify`, or summarize metagenome taxonomy with `summarize`. The +[sourmash lca tutorial](http://sourmash.readthedocs.io/en/latest/tutorials-lca.html) shows how to use the `lca classify` and `summarize` commands, and also provides guidance on building your own database. diff --git a/doc/command-line.md b/doc/command-line.md index 43c685170f..46d832aee4 100644 --- a/doc/command-line.md +++ b/doc/command-line.md @@ -231,7 +231,7 @@ using a collection of genomes with taxonomic information. ## `sourmash lca` subcommands -These commands use LCA databases (created with `index`, below, or +These commands use LCA databases (created with `lca index`, below, or prepared databases such as [genbank-k31.lca.json.gz, from the LCA tutorial](tutorials-lca.html). @@ -281,7 +281,7 @@ Example output: ### `sourmash lca gather` -The `sourmash lca gather` command classifies finds all non-overlapping +The `sourmash lca gather` command finds all non-overlapping matches to the query, similar to the `sourmash gather` command. This is specifically meant for metagenome and genome bin analysis. (See [Classifying Signatures](classifying-signatures.html) for more