ska

Split k-mer analysis – version 2

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

Science Score: 44.0%

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

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CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
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Academic publication links
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Committers with academic emails
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (15.1%) to scientific vocabulary

Keywords

alignment bioinformatics k-mer rust sequence ska

Last synced: 6 months ago · JSON representation ·

Repository

Split k-mer analysis – version 2

Basic Info

Host: GitHub
Owner: bacpop
License: apache-2.0
Language: Rust
Default Branch: master
Homepage: https://docs.rs/ska/latest/ska/
Size: 760 KB

Statistics

Stars: 88
Watchers: 6
Forks: 6
Open Issues: 9
Releases: 21

Topics

alignment bioinformatics k-mer rust sequence ska

Created over 3 years ago · Last pushed 7 months ago

Metadata Files

Readme License Citation

Split K-mer Analysis (version 2)

Description

This is a reimplementation of the SKA package in the rust language, by Johanna von Wachsmann, Simon Harris and John Lees. We are also grateful to have received user contributions from:

Romain Derelle
Tommi Maklin
Joel Hellewell
Timothy Russell
Nicholas Croucher
Dan Lu

Split k-mer analysis (version 2) uses exact matching of split k-mer sequences to align closely related sequences, typically small haploid genomes such as bacteria and viruses.

SKA can only align SNPs further than the k-mer length apart, and does not use a gap penalty approach or give alignment scores. But the advantages are speed and flexibility, particularly the ability to run on a reference-free manner (i.e. including accessory genome variation) on both assemblies and reads.

Citation

Romain Derelle, Johanna von Wachsmann, Tommi Mäklin, Joel Hellewell, Timothy Russell, Ajit Lalvani, Leonid Chindelevitch, Nicholas J. Croucher, Simon R. Harris, John A. Lees (2024). Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis. Genome Research, 34(10), 1661–1673.

https://genome.cshlp.org/content/34/10/1661.abstract

Documentation

Can be found at https://docs.rs/ska. We also have some tutorials available:

Installation

Choose from:

Download a binary from the releases.
Use cargo install ska or cargo add ska.
Use conda install -c bioconda ska2 (note the two!).
Build from source

For 2) or 4) you must have the rust toolchain installed.

OS X users

If you have an M1/M2 (arm64) Mac, we aren't currently automatically building binaries, so would recommend either option 2) or 4) 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" ./ska

Build from source

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

Differences from SKA1

Optimisations include:

Integer DNA encoding, optimised parsing from FASTA/FASTQ.
Faster dictionaries.
Full parallelisation of build phase.
Smaller, standardised input/output files. Faster to save/load.
Reduced memory footprint and increased speed with read filtering.

And other improvements:

IUPAC uncertainty codes for multiple copy split k-mers.
Uncertainty with self-reverse-complement split k-mers (palindromes).
Fully dynamic files (merge, delete samples).
Native VCF output for map.
Support for known strand sequence (e.g. RNA viruses).
Stream to STDOUT, or file with -o.
Simpler command line combining ska fasta, ska fastq, ska alleles and ska merge into the new ska build.
Option for single commands to run ska align or ska map.
New coverage model for filtering FASTQ files with ska cov.
Logging.
CI testing.

All of which make ska.rust run faster and with smaller file size and memory footprint than the original.

Planned features

Sparse data structure which will reduce space and make parallelisation more efficient. Issue #47.
'fastcall' mode. Issue #52.

Feature ideas (not definitely planned)

Add support for ambiguity in VCF output (ska map). Issue #5.
Non-serial loading of .skf files (for when they are very large). Issue #22.
Alternative mixture models for read error correction. Issue #50.

Things you can no longer do

Use k > 63 (shouldn't be necessary? Let us know if you need this and why).
ska annotate (use bedtools).
ska compare, ska humanise, ska info or ska summary (replaced by ska nk --full-info).
ska unique (you can parse ska nk --full-info if you want this functionality, but we didn't think it's used much).
ska type (use PopPUNK instead of MLST 🙂)
Ns are always skipped, and will not be found in any split k-mers.
.skf files are not backwards compatible with version 1.

Owner

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

Website: www.bacpop.org
Repositories: 20
Profile: https://github.com/bacpop

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

Citation (CITATION.cff)

cff-version: 1.2.0
message: If you use this software, please cite both the article from preferred-citation and the software itself.
authors:
  - family-names: Derelle
    given-names: Romain
  - family-names: von Wachsmann
    given-names: Johanna
  - family-names: Mäklin
    given-names: Tommi
  - family-names: Croucher
    given-names: Nicholas J.
  - family-names: Harris
    given-names: Simon R.
  - family-names: Lees
    given-names: John A.
title: Split K-mer Analysis (version 2)
version: 0.3.11
url: https://github.com/bacpop/ska.rust
date-released: '2024-09-25'
preferred-citation:
  authors:
    - family-names: Derelle
      given-names: Romain
    - family-names: von Wachsmann
      given-names: Johanna
    - family-names: Mäklin
      given-names: Tommi
    - family-names: Hellewell
      given-names: Joel
    - family-names: Russell
      given-names: Timothy
    - family-names: Lalvani
      given-names: Ajit
    - family-names: Chindelevitch
      given-names: Leonid
    - family-names: Croucher
      given-names: Nicholas J.
    - family-names: Harris
      given-names: Simon R.
    - family-names: Lees
      given-names: John A.
  title: Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis
  doi: 10.1101/gr.279449.124
  url: http://genome.cshlp.org/content/34/10/1661.abstract
  type: article
  pages: 1661-1673
  year: '2024'
  conference: {}
  publisher: {}

GitHub Events

Total

Create event: 6
Release event: 1
Issues event: 10
Watch event: 22
Delete event: 2
Member event: 2
Issue comment event: 65
Push event: 62
Pull request review comment event: 67
Pull request review event: 15
Pull request event: 13
Fork event: 2

Last Year

Create event: 6
Release event: 1
Issues event: 10
Watch event: 22
Delete event: 2
Member event: 2
Issue comment event: 65
Push event: 62
Pull request review comment event: 67
Pull request review event: 15
Pull request event: 13
Fork event: 2

Committers

Last synced: about 2 years ago

All Time

Total Commits: 234
Total Committers: 2
Avg Commits per committer: 117.0
Development Distribution Score (DDS): 0.013

Past Year

Commits: 216
Committers: 2
Avg Commits per committer: 108.0
Development Distribution Score (DDS): 0.014

Top Committers

Name	Email	Commits
John Lees	l**6@g**m	231
Tommi Mäklin	t**i@m**i	3

Committer Domains (Top 20 + Academic)

maklin.fi: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 47
Total pull requests: 56
Average time to close issues: about 1 month
Average time to close pull requests: 1 day
Total issue authors: 14
Total pull request authors: 6
Average comments per issue: 3.38
Average comments per pull request: 1.55
Merged pull requests: 47
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 10
Pull requests: 13
Average time to close issues: 20 days
Average time to close pull requests: 4 days
Issue authors: 8
Pull request authors: 4
Average comments per issue: 3.7
Average comments per pull request: 3.85
Merged pull requests: 8
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

johnlees (16)
rderelle (10)
danrlu (5)
PWSmit (3)
jvfe (1)
jdaeth274 (1)
vesa00 (1)
rrwick (1)
tmaklin (1)
kristyhoran (1)
cammo0p (1)
kebern (1)
maxlcummins (1)
taffners (1)

Pull Request Authors

johnlees (42)
apollis44 (9)
jhellewell14 (6)
rderelle (4)
vrbouza (2)
tmaklin (1)

Top Labels

Issue Labels

enhancement (17) bug (3) not planned (2) documentation (2)

Pull Request Labels

bug (2) documentation (2)

Packages

Total packages: 1
Total downloads:
- cargo 24,266 total

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 22
Total maintainers: 1

crates.io: ska

Split k-mer analysis

Homepage: https://bacpop.org/software/
Documentation: https://docs.rs/ska/
License: Apache-2.0
Latest release: 0.4.1
published 7 months ago

Versions: 22
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 24,266 Total

Rankings

Dependent repos count: 16.5%

Stargazers count: 19.1%

Forks count: 23.2%

Average: 28.1%

Dependent packages count: 36.1%

Downloads: 45.7%

Maintainers (1)

johnlees

Last synced: 6 months ago

Dependencies

.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/codecov.yml actions

actions-rs/grcov v0.1.5 composite
actions-rs/toolchain v1 composite
actions/checkout v3 composite
codecov/codecov-action v3.1.0 composite

.github/workflows/release.yml actions

actions-rs/toolchain v1 composite
actions/checkout v3 composite
actions/checkout v2 composite
actions/download-artifact v2 composite
actions/upload-artifact v3 composite
katyo/publish-crates v1 composite
softprops/action-gh-release v1 composite

.github/workflows/version.yml actions

actions/checkout v3 composite

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 0.8.2
ciborium 0.2.0
clap 4.0.27
hashbrown 0.12
indicatif 0.17.2
log 0.4.17
ndarray 0.15.6
needletail 0.4.1
noodles-vcf 0.22.0
num-traits 0.2.15
num_cpus 1.0
rayon 1.5.3
regex 1.7.0
serde 1.0.147
simple_logger 4.0.0
snap 1.1.0

ska

Science Score: 44.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Split K-mer Analysis (version 2)

Description

Citation

Documentation

Installation

OS X users

Build from source

Differences from SKA1

Planned features

Feature ideas (not definitely planned)

Things you can no longer do

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

crates.io: ska

Rankings

Maintainers (1)

Dependencies