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[MRG] add some docs on search, gather, and lca methods (#393)
* Bump version and add note pointing to stable docs * add some docs on search, gather, and lca * updated some text * Fix formatting error * update sourmash lca output * upgrade the documentation a bunch * cleanup foo * address @taylorreiter comments * link to LCA databases * provide construction details
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# Classifying signatures: `search`, `gather`, and `lca` methods. | ||
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sourmash provides several different techniques for doing | ||
classification and breakdown of signatures. | ||
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## Searching for similar samples with `search`. | ||
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The `sourmash search` command is most useful when you are looking for | ||
high similarity matches to other signatures; this is the most basic use | ||
case for MinHash searching. The command takes a query signature and one | ||
or more search signatures, and finds all the matches it can above a particular | ||
threshold. | ||
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By default `search` will find matches with high [*Jaccard | ||
similarity*](https://en.wikipedia.org/wiki/Jaccard_index), which will | ||
consider all of the k-mers in the union of the two samples. | ||
Practically, this means that you will only find matches if there is | ||
both high overlap between the samples *and* relatively few k-mers that | ||
are disjoint between the samples. This is effective for finding genomes | ||
or transcriptomes that are similar but rarely works well for samples | ||
of vastly different sizes. | ||
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One useful modification to `search` is to calculate containment with | ||
`--containment` instead of the (default) similarity; this will find | ||
matches where the query is contained within the subject, but the | ||
subject may have many other k-mers in it. For example, if you are using | ||
a plasmid as a query, you would use `--containment` to find genomes | ||
that contained that plasmid. | ||
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See [the main sourmash | ||
tutorial](http://sourmash.readthedocs.io/en/latest/tutorials.html#make-and-search-a-database-quickly) | ||
for information on using `search` with and without `--containment`. | ||
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## Breaking down metagenomic samples with `gather` and `lca` | ||
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Neither search option (similarity or containment) is effective when | ||
comparing or searching with metagenomes, which typically have a | ||
mixture of many different genomes. While you might use containment to | ||
see if a query genome is present in one or more metagenomes, a common | ||
question to ask is the reverse: **what genomes are in my metagenome?** | ||
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We have implemented two algorithms in sourmash to do this. | ||
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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. | ||
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The other approach, `gather`, breaks a metagenome down into individual | ||
genomes based on greedy partitioning. Essentially, it takes a query | ||
metagenome and searches the database for the most highly contained | ||
genome; it then subtracts that match from the metagenome, and repeats. | ||
At the end it reports how much of the metagenome remains unknown. The | ||
[basic sourmash | ||
tutorial](http://sourmash.readthedocs.io/en/latest/tutorials.html#what-s-in-my-metagenome) | ||
has some sample output from using gather with GenBank. | ||
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Our preliminary benchmarking suggests that `gather` is the most accurate | ||
method available for doing strain-level resolution of genomes. More on that | ||
as we move forward! | ||
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## To do taxonomy, or not to do taxonomy? | ||
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By default, there is no structured taxonomic information available in | ||
sourmash signatures or SBT databases of signatures. Generally what | ||
this means is that you will have to provide your own mapping from a | ||
match to some taxonomic hierarchy. This is generally the case when | ||
you are working with lots of genomes that have no taxonomic | ||
information. | ||
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The `lca` subcommands, however, work with LCA databases, which contain | ||
taxonomic information by construction. This is one of the main | ||
differences between the `sourmash lca` subcommands and the basic | ||
`sourmash search` functionality. So the `lca` subcommands will generally | ||
output structured taxonomic information, and these are what you should look | ||
to if you are interested in doing classification. | ||
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It's important to note that taxonomy based on k-mers is very, very | ||
specific and if you get a match, it's pretty reliable. On the | ||
converse, however, k-mer identification is very brittle with respect | ||
to evolutionary divergence, so if you don't get a match it may only mean | ||
that the particular species isn't known. | ||
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## What commands should I use? | ||
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It's not always easy to figure that out, we know! We're thinking about | ||
better tutorials and documentation constantly. | ||
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We suggest the following approach: | ||
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* build some signatures and do some searches, to get some basic familiarity | ||
with sourmash; | ||
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* explore the available databases; | ||
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* then ask questions [via the issue tracker](https://github.com/dib-lab/sourmash/issues) and we will do our best to help you out! | ||
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This helps us figure out what people are actually interested in doing, and | ||
any help we provide via the issue tracker will eventually be added into the | ||
documentation. |
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