C. Titus Brown

in https://github.com/dib-lab/genome-grist/pull/85 we added two figures, one about coverage and one about abundance. we could add another plot that estimates ANI of reads to genome, or something. not sure what...

choose abundtrim memory parameters based on k-mer counting estimates

9

ref #51 Mo - so, khmer pre-allocate the memory even there's no need for it? titus:speech_balloon: 9 minutes ago Yes - after all, how do you know how many kmers...

figure out how to retain/extract unmapped reads, too.

2

we already have the unmapped hashes, due to the split function. for unmapped reads... what do we want to do with them? * feed them from a DNA query into...

https://github.com/wwood/kingfisher-download

it's a little bit circuitous, but for people that really want taxonomic classification of _reads_ and not entire data sets, we can do that by identifying their best-mapping genome(s) :)

* run `git log --oneline v0.6.1..` to get list of merges since last release * cut a new tag w/release notes over at https://github.com/dib-lab/genome-grist/releases/new - mark it as pre-release *...

swipe marisa's image from 2/8/21 for README

1

@marisalim has a nice colorful image of the genome-grist workflow that we should co-opt and put in the README

provide non-mapping based summaries, too

1

the taxonomic analysis in #35 and the protein comparisons in #40 as well as the sample summaries in #42 can all be usefully done immediately after the gather and genome...

add summary reporting for multiple samples

1

using https://github.com/dib-lab/genome-grist/pull/56, add a notebook or output for summary reporting on sample details. some code for loading and displaying: ``` import itables import glob import yaml import pandas x =...

comparing and evaluating DNA vs protein matches

5

So, I did a thing, and I don't really know how to evaluate it. Thoughts welcome! ## summary: DNA and protein so I gristed a bunch of the Northen data...