C. Titus Brown

working on fixing this up for fastgather here: https://hackmd.io/aYV5HvqNRK63WDzB2ABOYw

# From raw metagenome reads to phyloseq taxonomy table using sourmash gather and sourmash taxonomy (STAMPS 2024) Updated by CTB 7/24/24 for STAMPS: uses `fastgather` now. ## Introduction to `gather`...

Here's all the R code in that tutorial, primed to work with the CSV files from the attached zip file and the following conda install: ``` conda create -y -n...

updated so it _should_ work with both `gather` and `fastgather` CSV files: ``` library(tidyverse) library(phyloseq) # create a metadata table ------------------------------------------------- # create a metadata that has the SRR run...

ref https://github.com/sourmash-bio/sourmash/issues/3339

to produce a standalone manifest from the `mf.csv` files (and also probably from the zip files), do ``` sourmash sig collect -F csv *.mf.csv -o combined.mf.csv --abspath ```

and on a further somewhat unrelated note, `fastgather` took even less time than sketching.

and even more so, to add a sketch it is faster to * add a sequence to the fa gz file * rerun manysketch than it is to run `sig...

Try using `--singleton` - that should do what you want :). See: [link](https://github.com/sourmash-bio/sourmash_plugin_branchwater/tree/main/doc#singleton-sketching)

`singlesketch` in sourmash_plugin_branchwater is even faster now ;)