Data

Tools

Indexes

Applications

Experiments

Open Source Science

spacegraphcats

Indexing & querying large assembly graphs -- in space, no one can hear you miao!

https://github.com/spacegraphcats/spacegraphcats

Science Score: 33.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: arxiv.org, zenodo.org
  • ✓
    Committers with academic emails
    4 of 16 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.8%) to scientific vocabulary

Keywords

bioinformatics k-mers metagenomics

Keywords from Contributors

taxonomic-classification workflows workflow-management
Last synced: 10 months ago · JSON representation

Repository

Indexing & querying large assembly graphs -- in space, no one can hear you miao!

Basic Info
Statistics
  • Stars: 119
  • Watchers: 11
  • Forks: 15
  • Open Issues: 118
  • Releases: 16
Topics
bioinformatics k-mers metagenomics
Created about 10 years ago · Last pushed over 2 years ago
Metadata Files
Readme License

README.md

spacegraphcats

Test codecov DOI PyPI

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 University of Utah, the Lab for Data Intensive Biology at UC Davis, and Dr. Felix Reidl at Birkbeck University of London. Initial development of spacegraphcats was generously supported by the Moore Foundation's Data Driven Discovery Initiative.

spacegraphcats graph

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 and the run guide.

For help or support with this software, please file an issue on GitHub. Thank you!

Quickstart

There are two quickstart examples available! Please see dory-example and twofoo-example. The latter example includes a snakemake Snakefile.

Notable dependencies

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.

spacegraphcats also uses functionality from khmer and sourmash.

Citation information

See the Genome Biology publication Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity, 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.

The graph denoising code for removing low-abundance pendants from BCALM cDBGs is in function contract_degree_two in cdbg/bcalmtogxt.py.

Part of the indexPieces code for indexing cDBG nodes by dominating nodes is cdbg/indexcdbgby_kmer.py. The remainder is implemented in search, below.

The search code for extracting query neighborhoods is in search/querybysequence.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 and search/search_utils.py, get_reads_by_cdbg, respectively.

Owner

  • Name: spacegraphcats
  • Login: spacegraphcats
  • Kind: organization

In space nobody can hear you meow! (and graphs)

GitHub Events

Total
  • Watch event: 2
Last Year
  • Watch event: 2

Committers

Last synced: over 3 years ago

All Time
  • Total Commits: 1,114
  • Total Committers: 16
  • Avg Commits per committer: 69.625
  • Development Distribution Score (DDS): 0.299
Top Committers
Name Email Commits
C. Titus Brown t****s@i****g 781
Mike O'Brien m****3@n****u 108
Dominik Moritz d****z@g****m 99
Felix Reidl f****l@g****m 50
Mike O'Brien s****b@g****m 28
ubik r****l@c****e 13
dependabot[bot] 4****]@u****m 11
Taylor Reiter t****r@g****m 9
Tessa Pierce n****e@g****m 4
Blair D. Sullivan b****n@n****u 3
Yosuke Mizutani m****j@g****m 2
mike m****e@o****u 2
Ubuntu u****u@i****l 1
Kevinlega k****z@g****m 1
Ubuntu u****u@i****l 1
Tessa Pierce b****s@u****m 1
Committer Domains (Top 20 + Academic)
ncsu.edu: 2 ip-172-31-15-1.us-east-2.compute.internal: 1 ip-172-31-15-109.us-east-2.compute.internal: 1 oak.csc.ncsu.edu: 1 cs.rwth-aachen.de: 1 idyll.org: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 55
  • Total pull requests: 64
  • Average time to close issues: 3 months
  • Average time to close pull requests: about 2 months
  • Total issue authors: 11
  • Total pull request authors: 5
  • Average comments per issue: 2.73
  • Average comments per pull request: 2.17
  • Merged pull requests: 40
  • Bot issues: 0
  • Bot pull requests: 31
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ctb (22)
  • taylorreiter (20)
  • maureenbug (3)
  • ccbaumler (2)
  • drtamermansour (2)
  • skafaie (1)
  • christygrettenberger (1)
  • alarasutcu (1)
  • mogproject (1)
  • jessicalumian (1)
  • dnolin13 (1)
Pull Request Authors
  • dependabot[bot] (33)
  • ctb (27)
  • taylorreiter (4)
  • ccbaumler (2)
  • mogproject (1)
Top Labels
Issue Labels
documentation (4) Results (2) v2.0 (2) error message (1) papers (1) enhancement (1)
Pull Request Labels
dependencies (33) python (22) github_actions (11) Results (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 18 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 15
  • Total maintainers: 1
pypi.org: spacegraphcats

tools for biological assembly graph neighborhood analysis

  • Versions: 15
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 18 Last month
Rankings
Stargazers count: 6.8%
Forks count: 9.6%
Dependent packages count: 10.1%
Average: 15.7%
Dependent repos count: 21.6%
Downloads: 30.5%
Maintainers (1)
titus
Last synced: 11 months ago

Dependencies

environment.yml conda
  • bbhash >=0.5.4
  • bcalm 2.2.3.*
  • click >=8.1.2,<9
  • khmer 3.0.0a3.*
  • mamba >=0.22.1
  • numpy
  • pyflakes
  • pytest 5.3.2.*
  • screed >=1.0.5,<2
  • snakemake-minimal 7.3.8.*
  • sortedcontainers 2.1.0.*
  • sourmash >=4.2.2,<5
requirements.txt pypi
  • bbhash >=0.5
  • black *
  • click >=8.1.2,<9
  • flake8 *
  • khmer *
  • numpy *
  • pandas *
  • pre-commit *
  • pytest >=5.1.2
  • pytest-dependency *
  • screed *
  • snakemake ==7.3.8
  • sortedcontainers *
  • sourmash >=4.2.2,<5
setup.py pypi
  • bbhash *
  • click *
  • khmer *
  • numpy *
  • pytest *
  • screed *
  • snakemake ==7.3.8
  • sortedcontainers *
  • sourmash >=4.2.2,<5
.github/workflows/gh-pages.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
.github/workflows/run_tests.yml actions
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • codecov/codecov-action v3 composite
  • conda-incubator/setup-miniconda v2 composite