# spacegraphcats
 [](https://codecov.io/gh/spacegraphcats/spacegraphcats) [](https://zenodo.org/badge/latestdoi/58208221) <a href="https://pypi.org/project/spacegraphcats/"><img alt="PyPI" src="https://badge.fury.io/py/spacegraphcats.svg"></a>
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](https://github.com/TheoryInPractice/) lab at University of Utah, the
[Lab for Data Intensive Biology](https://github.com/dib-lab/) at UC Davis, and
[Dr. Felix Reidl](https://www.dcs.bbk.ac.uk/about/people/academic-staff/felix/) at Birkbeck University of London.
Initial development of spacegraphcats was generously supported by the Moore Foundation's
[Data Driven Discovery Initiative](https://www.moore.org/initiative-strategy-detail?initiativeId=data-driven-discovery).
## Documentation
This README file contains quickstart information.
For use cases and other information, please see the spacegraphcats documentation at https://spacegraphcats.github.io/spacegraphcats.
## Installation and execution quickstart
See [installation instructions](https://github.com/spacegraphcats/spacegraphcats/blob/latest/doc/00-installing-spacegraphcats.md) and [the run guide](https://github.com/spacegraphcats/spacegraphcats/blob/latest/doc/01-running-spacegraphcats.md).
For help or support with this software, please
[file an issue on GitHub](https://github.com/spacegraphcats/spacegraphcats/issues). Thank
you!
### Quickstart
There are two quickstart examples available! Please see
[dory-example](https://github.com/spacegraphcats/spacegraphcats-dory-example)
and
[twofoo-example](https://github.com/spacegraphcats/spacegraphcats-twofoo-example). The
latter example includes
[a snakemake Snakefile](https://snakemake.readthedocs.io/en/stable/).
### Notable dependencies
spacegraphcats uses code from
[BBHash](https://github.com/rizkg/BBHash), a C++ library for building
minimal perfect hash functions (Guillaume Rizk, Antoine Limasset,
Rayan Chikhi; see
[Limasset et al., 2017, arXiv](https://arxiv.org/abs/1702.03154), as
wrapped by [pybbhash](https://github.com/dib-lab/pybbhash).
spacegraphcats also uses functionality from
[khmer](https://github.com/dib-lab/khmer/) and
[sourmash](https://github.com/dib-lab/sourmash).
## Citation information
See the Genome Biology publication [Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02066-4), Brown et al., 2020, doi: https://doi.org/10.1186/s13059-020-02066-4.
## Pointers to interesting code
### Interesting algorithms
The `rdomset` code for efficently calculating a dominating set of a graph
at a given radius R is in [spacegraphcats/catlas/rdomset.py](https://github.com/spacegraphcats/spacegraphcats/blob/latest/spacegraphcats/catlas/rdomset.py).
The graph denoising code for removing low-abundance pendants from
BCALM cDBGs is in function `contract_degree_two` in
[cdbg/bcalm_to_gxt.py](https://github.com/spacegraphcats/spacegraphcats/blob/latest/spacegraphcats/cdbg/bcalm_to_gxt.py).
Part of the `indexPieces` code for indexing cDBG nodes by dominating
nodes is
[cdbg/index_cdbg_by_kmer.py](https://github.com/spacegraphcats/spacegraphcats/blob/latest/spacegraphcats/cdbg/index_cdbg_by_kmer.py). The
remainder is implemented in `search`, below.
The `search` code for extracting query neighborhoods is in
[search/query_by_sequence.py](https://github.com/spacegraphcats/spacegraphcats/blob/latest/spacegraphcats/search/query_by_sequence.py);
see especially the call to `kmer_idx.count_cdbg_matches(...)`.
### 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
[cdbg/label_cdbg.py](https://github.com/spacegraphcats/spacegraphcats/blob/latest/spacegraphcats/cdbg/index_reads.py)
and
[search/search_utils.py](https://github.com/spacegraphcats/spacegraphcats/blob/latest/spacegraphcats/search/search_utils.py),
`get_reads_by_cdbg`, respectively.
Raw data
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"author": "C. Titus Brown, Dominik Moritz, Michael P. O'Brien, Felix Reidl, Taylor Reiter, Yosuke Mizutani, and Blair D. Sullivan",
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"description": "# spacegraphcats\n\n [](https://codecov.io/gh/spacegraphcats/spacegraphcats) [](https://zenodo.org/badge/latestdoi/58208221) <a href=\"https://pypi.org/project/spacegraphcats/\"><img alt=\"PyPI\" src=\"https://badge.fury.io/py/spacegraphcats.svg\"></a>\n\n\nExplore large, annoying graphs using hierarchies of dominating sets - because\nin space, no one can hear you miao!\n\nThis is a collaboration between the\n[Theory In Practice](https://github.com/TheoryInPractice/) lab at University of Utah, the\n[Lab for Data Intensive Biology](https://github.com/dib-lab/) at UC Davis, and\n[Dr. Felix Reidl](https://www.dcs.bbk.ac.uk/about/people/academic-staff/felix/) at Birkbeck University of London. \nInitial development of spacegraphcats was generously supported by the Moore Foundation's\n[Data Driven Discovery Initiative](https://www.moore.org/initiative-strategy-detail?initiativeId=data-driven-discovery).\n\n\n\n## Documentation\n\nThis README file contains quickstart information.\nFor use cases and other information, please see the spacegraphcats documentation at https://spacegraphcats.github.io/spacegraphcats.\n\n## Installation and execution quickstart\n\nSee [installation instructions](https://github.com/spacegraphcats/spacegraphcats/blob/latest/doc/00-installing-spacegraphcats.md) and [the run guide](https://github.com/spacegraphcats/spacegraphcats/blob/latest/doc/01-running-spacegraphcats.md).\n\nFor help or support with this software, please\n[file an issue on GitHub](https://github.com/spacegraphcats/spacegraphcats/issues). Thank\nyou!\n\n### Quickstart\n\nThere are two quickstart examples available! Please see\n[dory-example](https://github.com/spacegraphcats/spacegraphcats-dory-example)\nand\n[twofoo-example](https://github.com/spacegraphcats/spacegraphcats-twofoo-example). The\nlatter example includes\n[a snakemake Snakefile](https://snakemake.readthedocs.io/en/stable/).\n\n### Notable dependencies\n\nspacegraphcats uses code from\n[BBHash](https://github.com/rizkg/BBHash), a C++ library for building\nminimal perfect hash functions (Guillaume Rizk, Antoine Limasset,\nRayan Chikhi; see\n[Limasset et al., 2017, arXiv](https://arxiv.org/abs/1702.03154), as\nwrapped by [pybbhash](https://github.com/dib-lab/pybbhash).\n\nspacegraphcats also uses functionality from\n[khmer](https://github.com/dib-lab/khmer/) and\n[sourmash](https://github.com/dib-lab/sourmash).\n\n## Citation information\n\nSee the Genome Biology publication [Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02066-4), Brown et al., 2020, doi: https://doi.org/10.1186/s13059-020-02066-4.\n\n## Pointers to interesting code\n\n### Interesting algorithms\n\nThe `rdomset` code for efficently calculating a dominating set of a graph\nat a given radius R is in [spacegraphcats/catlas/rdomset.py](https://github.com/spacegraphcats/spacegraphcats/blob/latest/spacegraphcats/catlas/rdomset.py).\n\nThe graph denoising code for removing low-abundance pendants from\nBCALM cDBGs is in function `contract_degree_two` in\n[cdbg/bcalm_to_gxt.py](https://github.com/spacegraphcats/spacegraphcats/blob/latest/spacegraphcats/cdbg/bcalm_to_gxt.py).\n\nPart of the `indexPieces` code for indexing cDBG nodes by dominating\nnodes is\n[cdbg/index_cdbg_by_kmer.py](https://github.com/spacegraphcats/spacegraphcats/blob/latest/spacegraphcats/cdbg/index_cdbg_by_kmer.py). The\nremainder is implemented in `search`, below.\n\nThe `search` code for extracting query neighborhoods is in\n[search/query_by_sequence.py](https://github.com/spacegraphcats/spacegraphcats/blob/latest/spacegraphcats/search/query_by_sequence.py);\nsee especially the call to `kmer_idx.count_cdbg_matches(...)`.\n\n### Interesting library functionality\n\nCode for indexing large FASTQ/FASTA read files by cDBG unitig, and\nextracting the reads corresponding to individual unitigs from BGZF\nfiles, is available in\n[cdbg/label_cdbg.py](https://github.com/spacegraphcats/spacegraphcats/blob/latest/spacegraphcats/cdbg/index_reads.py)\nand\n[search/search_utils.py](https://github.com/spacegraphcats/spacegraphcats/blob/latest/spacegraphcats/search/search_utils.py),\n`get_reads_by_cdbg`, respectively.\n\n\n",
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