-
ref ANI estimation PR #1788
I've been using our forthcoming ANI utilities to estimate pairwise ANI between GTDB genomes. From these data, we can examine the average containment --> ANI relationshi…
-
In re this paper,
[Debiasing FracMinHash and deriving confidence intervals for mutation rates across a wide range of evolutionary distances](https://www.biorxiv.org/content/10.1101/2022.01.11.47587…
-
@drtamermansour asked some questions on slack about how FracMinHash signatures with different scaled values are handled in practice, and I took a look in the docs and couldn't find anything that was c…
-
curious how well our underlying infrastructure can work for handling other kinds of fracminhash sequences! maybe could be explored using plugins.
https://github.com/St4NNi/jam-rs
ctb updated
11 months ago
-
per https://github.com/sourmash-bio/sourmash/issues/267#issuecomment-1117633898
@dkoslicki says:
> In the FracMinHash sketches, does sourmash save the k-mers that led to the hash values, or just t…
-
https://hackmd.io/RScxLBU-SCiEjdNHrJql5w
# FracMinHash vs MinHash pseudocode
## FracMinHash
Here the `scaled` parameter is tunable, and `H` is the size of the hash space (e.g. 2**64).
Note…
-
as plugins proliferate (good? bad? who knows!) there seems to be a need for providing better docs and functions for plugins to make use of sourmash library code.
areas where I see this need most cl…
-
Hi,
Could you help me to understand how QueryContainmentAni and MatchContainmentAni are calculated?
Given the use of exact kmer matches, I would assume that the ANI between a query kmer and a re…
-
revisiting a (5 yro :) conversation about interoperability https://github.com/marbl/Mash/issues/27 after some discussions on slack with @kescobo on [µbioinfo slack](https://microbial-bioinfo.slack.com…
-
$P$(observe k events) =
Here the parameter $\lambda = \frac{M}{S}$ is the expected number of hashes
for $M$ k-mers at a scaled of $S$.
$P$(k hashes for M k-mers with scaled S) = ${\exp(-M /…