Explore large, annoying graphs using hierarchies of dominating sets - because in space, no one can hear you miao!
This is a collaboration between the Theory In Practice lab at NC State and the Lab for Data Intensive Biology at UC Davis, generously supported by the Moore Foundation's Data Driven Discovery Initiative.
Installation and execution quickstart
For help or support with this software, please file an issue on GitHub. Thank you!
spacegraphcats uses code from BBHash, a C++ library for building minimal perfect hash functions (Guillaume Rizk, Antoine Limasset, Rayan Chikhi; see Limasset et al., 2017, arXiv, as wrapped by pybbhash.
This is pre-publication code; a manuscript is in preparation. Please contact the authors for the current citation information if you wish to use it and cite it.
Pointers to interesting code
rdomset code for efficently calculating a dominating set of a graph
at a given radius R is in spacegraphcats/catlas/rdomset.py.
The graph denoising code for removing low-abundance pendants from
BCALM cDBGs is in function
Part of the
indexPieces code for indexing cDBG nodes by dominating
remainder is implemented in
search code for extracting query neighborhoods is in
see especially the call to
Interesting library functionality
Code for indexing large FASTQ/FASTA read files by cDBG unitig, and
extracting the reads corresponding to individual unitigs from BGZF
files, is available in