Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/bacpop/sketchlib.rust

Fast sequence distance estimates

https://github.com/bacpop/sketchlib.rust

Science Score: 39.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 8 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.7%) to scientific vocabulary

Keywords

bioinformatics genomics k-mer sketching
Last synced: 10 months ago · JSON representation

Repository

Fast sequence distance estimates

Basic Info
  • Host: GitHub
  • Owner: bacpop
  • License: apache-2.0
  • Language: Rust
  • Default Branch: main
  • Homepage: https://docs.rs/sketchlib
  • Size: 5.2 MB
Statistics
  • Stars: 15
  • Watchers: 6
  • Forks: 4
  • Open Issues: 12
  • Releases: 8
Topics
bioinformatics genomics k-mer sketching
Created over 2 years ago · Last pushed 11 months ago
Metadata Files
Readme License

README.md

sketchlib.rust

Cargo Build & Test Clippy check docs.rs codecov Crates.io GitHub release (latest SemVer) <!-- badges: end -->

Description

This is a reimplementation and extension of pp-sketchlib in the rust language. This version is optimised for larger sample numbers, particularly allowing subsets of samples to be compared.

v0.2.0 is the first stable release. We intend to keep the file format unchanged after this point so sketch libraries will not need to be rebuilt.

Citation

No preprint or paper yet, but we rely on algorithms from:

bindash (written by XiaoFei Zhao):\ Zhao, X. BinDash, software for fast genome distance estimation on a typical personal laptop.\ Bioinformatics 35:671–673 (2019).\ doi:10.1093/bioinformatics/bty651

ntHash (written by Hamid Mohamadi):\ Mohamadi, H., Chu, J., Vandervalk, B. P. & Birol, I. ntHash: recursive nucleotide hashing.\ Bioinformatics 32:3492–3494 (2016).\ doi:10.1093/bioinformatics/btw397

Documentation

See https://docs.rs/sketchlib

Installation

Choose from:

  1. Download a binary from the releases.
  2. Use cargo install sketchlib or cargo add sketchlib.
  3. Build from source

For 2) or 3) you must have the rust toolchain installed.

OS X users

If you have an M1-4 (arm64) Mac, we aren't currently automatically building binaries, so would recommend either option 2) or 3) for best performance.

If you get a message saying the binary isn't signed by Apple and can't be run, use the following command to bypass this:

xattr -d "com.apple.quarantine" ./sketchlib

Build from source

  1. Clone the repository with git clone.
  2. Run cargo install --path . or RUSTFLAGS="-C target-cpu=native" cargo install --path . to optimise for your machine.

Owner

  • Name: Bacterial population genetics
  • Login: bacpop
  • Kind: organization
  • Email: contact@bacpop.org
  • Location: United Kingdom

Pathogen Informatics and Modelling @ EMBL-EBI / Bacterial Evolutionary Epidemiology Group @ Imperial College London

GitHub Events

Total
  • Fork event: 1
  • Create event: 18
  • Commit comment event: 1
  • Release event: 7
  • Issues event: 23
  • Watch event: 11
  • Delete event: 6
  • Member event: 2
  • Issue comment event: 43
  • Push event: 74
  • Pull request review comment event: 21
  • Pull request review event: 19
  • Pull request event: 20
Last Year
  • Fork event: 1
  • Create event: 18
  • Commit comment event: 1
  • Release event: 7
  • Issues event: 23
  • Watch event: 11
  • Delete event: 6
  • Member event: 2
  • Issue comment event: 43
  • Push event: 74
  • Pull request review comment event: 21
  • Pull request review event: 19
  • Pull request event: 20

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 14
  • Total pull requests: 8
  • Average time to close issues: 8 months
  • Average time to close pull requests: 4 days
  • Total issue authors: 4
  • Total pull request authors: 1
  • Average comments per issue: 1.14
  • Average comments per pull request: 1.5
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 8
  • Pull requests: 8
  • Average time to close issues: 3 months
  • Average time to close pull requests: 4 days
  • Issue authors: 4
  • Pull request authors: 1
  • Average comments per issue: 0.88
  • Average comments per pull request: 1.5
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • johnlees (9)
  • valflanza (2)
  • tgttunstall (1)
  • cizydorczyk (1)
  • CarmenGenpax (1)
  • tmaklin (1)
Pull Request Authors
  • johnlees (8)
  • johannahelene (3)
  • vrbouza (2)
Top Labels
Issue Labels
bug (3) good first issue (2) wontfix (1) documentation (1) functionality (1)
Pull Request Labels
functionality (2) enhancement (1) bug (1)

Packages

  • Total packages: 1
  • Total downloads:
    • cargo 5,150 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 9
  • Total maintainers: 1
crates.io: sketchlib

Genome and amino-acid sketching

  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 5,150 Total
Rankings
Dependent repos count: 23.5%
Dependent packages count: 31.2%
Average: 50.0%
Downloads: 95.4%
Maintainers (1)
johnlees
Last synced: 10 months ago

Dependencies

Cargo.toml cargo
  • assert_fs 1.0.10 development
  • predicates 2.1.5 development
  • pretty_assertions 1.3.0 development
  • snapbox 0.4.3 development
  • ahash >=0.8.7
  • anyhow 1.0
  • arrayref 0.3
  • ciborium 0.2
  • clap 4.5
  • hashbrown 0.14
  • indicatif 0.17
  • log 0.4
  • memmap2 0.9
  • needletail 0.5
  • num_cpus 1.0
  • rayon 1.8
  • regex 1.10
  • serde 1.0
  • simple_logger 4
  • snap 1.1
.github/workflows/ci.yml actions
  • actions/checkout v3 composite
.github/workflows/clippy.yml actions
  • actions-rs/clippy-check v1 composite
  • actions-rs/toolchain v1 composite
  • actions/checkout v1 composite
.github/workflows/version.yml actions
  • actions/checkout v3 composite
.github/workflows/codecov.yml actions
  • actions-rs/toolchain v1 composite
  • actions/checkout v3 composite
  • codecov/codecov-action v5.1.2 composite
.github/workflows/release.yml actions
  • actions-rs/toolchain v1 composite
  • actions/checkout v3 composite
  • actions/checkout v2 composite
  • actions/download-artifact v4 composite
  • actions/upload-artifact v4 composite
  • katyo/publish-crates v1 composite
  • softprops/action-gh-release v1 composite