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slides from a lab meeting on spacegraphcats internals #313

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ctb opened this issue Oct 19, 2020 · 4 comments
Open

slides from a lab meeting on spacegraphcats internals #313

ctb opened this issue Oct 19, 2020 · 4 comments
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ctb commented Oct 19, 2020

https://hackmd.io/@ctb/BkDE7msPv
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ctb commented Oct 19, 2020

notes --

blight came up a few times, of course!

Representation of k-mer sets using spectrum-preserving string sets
https://www.biorxiv.org/content/10.1101/2020.01.07.896928v2

ripgrep discussion of indexing
BurntSushi/ripgrep#1497

and also:
"""in case it’s not already on your mind, supertranscripts + protein k-mers would also smooth the rough edges of cross species analyses (or even within-species for really heterozygous species)"""

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ctb commented Oct 19, 2020

the ripgrep discussion also talks a bit about bloom filters and other details here -- BurntSushi/ripgrep#1518

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ctb commented Oct 19, 2020

Tamer suggests using straight-up grep. I toyed with this, but I think grep is fundamentally going to be linear time and I (at least in theory) would like to be able to do lots of small queries quickly. I also want to avoid any shell calls.

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ctb commented Oct 19, 2020

aaaaan of course luiz weighs in on the OTHER conversation with a pointer ...back to bioinformatics 😂

especially:
Data structures based on k-mers for querying large collections of sequencing datasets
https://www.biorxiv.org/content/10.1101/866756v1

@taylorreiter taylorreiter mentioned this issue Apr 30, 2021
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taylorreiter added a commit that referenced this issue Apr 30, 2021
@taylorreiter
add slideshow from #313 to dev guide
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ctb added a commit that referenced this issue May 21, 2021
@taylorreiter @ctb
[MRG] add documentation and mkdocs site for spacegraphcats (#392)
cd0ab0f 
* start adding docs for use cases and viz, rename current so ordered

* update links to install doc with new name

* add bandage viz

* start primer on metagenome analysis and graphs

* add placeholder for another use case

* revise section for working with assembly graphs

* add mkdocs init

* add mkdoc workflow

* update file linkers

* tmp change icon to school to troubleshoot

* update mkdocs logo, site url

* start landing page

* switch build branch from tr

* update developers guide to new files, new file names

* add slideshow from #313 to dev guide

* start parameters doc

* add CMAG

* change back to build on tr_doc branch for now

* add params to mkdocs

* add bin completion use case

* fix spacing for lists

* update output files

* fig placeholder for viz catlas

* fill in usecases more

* Update doc/01-running-spacegraphcats.md

* Update doc/02-spacegraphcats-use-cases.md

* Update doc/04-spacegraphcats-parameters.md

* address titus feedback

* woops don't delete 01-running-spacegraphcats.md

* start ARG tutorial

* finish ARG workflow

* add untar seq files

* add bandage output folder

* typo

* add internal command dag and description of test datasets

* arrange as alpha functionality, add multifasta query and build out hashval query

* add graphgrep

* try and slurp in the protein stuff

* separate alpha functionality from use cases

* start snakemake workflow integration

* add ani to params

* add col description for results.csv

* add extract reads overview

* at least say something about click CLI

* update felix and blairs info, link to docs in README

* make snakemake docs...passable

* add genome grist link

* switch to latest

* update readme moore ref

* titus' suggestions

* more titus typos

* update index affiliations

* Update doc/05-alpha-spacegraphcats.md

Co-authored-by: C. Titus Brown <titus@idyll.org>

* add link to 372

Co-authored-by: C. Titus Brown <titus@idyll.org>

* Update doc/05-alpha-spacegraphcats.md

Co-authored-by: C. Titus Brown <titus@idyll.org>

* typo

* /usr instead or usr

* add run commands to tests

* add dory_k21 files

* range for conda install sourmash

* Update doc/02-spacegraphcats-use-cases.md

Co-authored-by: C. Titus Brown <titus@idyll.org>

* Update doc/developing-spacegraphcats.md

Co-authored-by: C. Titus Brown <titus@idyll.org>

Co-authored-by: C. Titus Brown <titus@idyll.org>
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