C. Titus Brown
C. Titus Brown
mixtureS: a novel tool for bacterial strain genome reconstruction from reads https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btaa728/5893551?redirectedFrom=fulltext Abstract: >Motivation >It is essential to study bacterial strains in environmental samples. Existing methods and tools often depend...
it would be nice to have a machine-readable file containing information about k-mer size, etc. - maybe a YAML file?
@taylorreiter is doing cool stuff with running lots of spacegraphcats jobs inside of snakemake using --outdir etc. would be nice to provide an example with the sgc documentation.
right now spacegraphcats steps do not use conda environments. this is relatively easy to fix. should we? it would work the same was as in charcoal where it would be...
ref #282 think about how to track how many hashes CANNOT be interpreted this way; may involve restructuring scripts, or something.
[KOMB: Taxonomy-oblivious Characterization of Metagenome Dynamics via K-core Decomposition](https://www.biorxiv.org/content/10.1101/2020.05.21.109587v1) Background: Taxonomic classification of microbiomes has provided tremendous insight into the underlying genome dynamics of microbial communities but has relied on...
[PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007732) Abstract The use of comparative genomics for functional, evolutionary, and epidemiological studies requires methods to classify gene families in terms of...
ref #263 [see comment](https://github.com/spacegraphcats/spacegraphcats/pull/264#issuecomment-581143121) - > we could include the md5sum of the query and (some part of) the catlas, which would definitely distinguish them.
a few thoughts on unnecessary duplication of files and/or other space-saving ideas -- * `{catlas_base}/bcalm.{catlas_base}.k{ksize}.unitigs.fa` can be designated as `temporary`- it's only used once. * not sure this is fixable,...