lorikeet-genome

Strain resolver for metagenomics

https://github.com/rhysnewell/lorikeet

Science Score: 77.0%

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

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
Found 1 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
8 of 13 committers (61.5%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (13.1%) to scientific vocabulary

Last synced: 6 months ago · JSON representation ·

Repository

Strain resolver for metagenomics

Basic Info

Host: GitHub
Owner: rhysnewell
License: agpl-3.0
Language: Rust
Default Branch: master
Size: 31.3 MB

Statistics

Stars: 78
Watchers: 5
Forks: 10
Open Issues: 14
Releases: 20

Created almost 7 years ago · Last pushed over 1 year ago

Metadata Files

Readme License Citation

Lorikeet

Lorikeet is a within-species variant analysis pipeline for metagenomic communities that utilizes both long and short reads. Lorikeet utilizes a re-implementaion of the GATK HaplotypeCaller algorithm, performing local re-assembly of potentially active regions within candidate genomes. Called variants can be clustered into likely strains using a combination of UMAP and HDBSCAN.

Documentation

For detailed documentation of Lorikeet and the various algorithms and concepts it touches on please visit the Lorikeet Docs

Quick Start

Installation

Lorikeet is distributed via Crates.io https://crates.io/crates/lorikeet-genome. Additional packages can be downloaded via conda using the lorikeet.yml file provided. Ensure that cargo is installed on your system:

bash curl https://sh.rustup.rs -sSf | sh

Then install lorikeet:

bash cargo install lorikeet-genome

Alongside required packages:

bash conda env create -f lorikeet.yml -n lorikeet conda activate lorikeet

Usage

Input can either be reads and reference genome, or MAG. Or a BAM file and associated genome.

``` Strain genotyping analysis for metagenomics

Usage: lorikeet ...

Main subcommands: genotype Experimental Resolve strain-level genotypes of MAGs from microbial communities consensus Creates consensus genomes for each input reference and for each sample call Performs variant calling with no downstream analysis evolve Calculate dN/dS values for genes from read mappings

Other options: -V, --version Print version information

Rhys J. P. Newell ```

Call variants from bam:

lorikeet call --bam-files my.bam --longread-bam-files my-longread.bam --genome-fasta-directory genomes/ -x fna --bam-file-cache-directory saved_bam_files --output-directory lorikeet_out/ --threads 10 --plot

Call variants from short reads and longread bam files:

lorikeet call -r input_genome.fna -1 forward_reads.fastq -2 reverse_reads.fastq -l longread.bam

Shell completion

Completion scripts for various shells e.g. BASH can be generated. For example, to install the bash completion script system-wide (this requires root privileges):

lorikeet shell-completion --output-file lorikeet --shell bash mv lorikeet /etc/bash_completion.d/

It can also be installed into a user's home directory (root privileges not required):

lorikeet shell-completion --shell bash --output-file /dev/stdout >>~/.bash_completion

In both cases, to take effect, the terminal will likely need to be restarted. To test, type lorikeet ca and it should complete after pressing the TAB key.

License

Code is GPL-3.0

Owner

Name: Rhys Newell
Login: rhysnewell
Kind: user
Location: Sydney, Australia
Company: Microba LifeSciences

Website: rhysnewell.github.io
Twitter: rhysnewell
Repositories: 11
Profile: https://github.com/rhysnewell

Bioinformatics Software Engineer @ Microba. Awaiting for my PhD to be examined. Specialises in software development and analysis of big genomic data

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Newell
    given-names: Rhys J. P.
    orcid: https://orcid.org/0000-0002-1300-6116
  - family-names: McMaster
    given-names: Eilish S.
    orcid: https://orcid.org/0000-0002-7415-8690
  - family-names: Craig
    given-names: Philip
  - family-names: Boden
    given-names: Mikael
    orcid: https://orcid.org/0000-0003-3548-268X
  - family-names: Tyson
    given-names: Gene W.
    orcid: https://orcid.org/0000-0001-8559-9427
  - family-names: Woodcroft
    given-names: Ben J.
    orcid: https://orcid.org/0000-0003-0670-7480
title: "Lorikeet: strain-resolved metagenome analysis using local reassembly"
version: 0.8.2
doi: 10.5281/zenodo.10275469
date-released: 2023-11-05

GitHub Events

Total

Issues event: 1
Watch event: 9
Issue comment event: 1

Last Year

Issues event: 1
Watch event: 9
Issue comment event: 1

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 1,867
Total Committers: 13
Avg Commits per committer: 143.615
Development Distribution Score (DDS): 0.446

Past Year

Commits: 76
Committers: 2
Avg Commits per committer: 38.0
Development Distribution Score (DDS): 0.079

Top Committers

Name	Email	Commits
rhysnewell	r**l@u**u	1,034
Rhys Newell	r**l@h**u	743
Rhys Newell	4**l@u**m	54
rhysnewell	r**l@u**u	11
Rhys Newell	r**l@m**m	6
Rhys Newell	n**9@c**u	4
Rhys Newell	s**1@p**u	4
Ben Woodcroft	b**t@g**m	2
Rhys Newell	s**1@h**u	2
Rhys Newell	n**9@c**u	2
Rhys Newell	s**1@c**u	2
Ben Woodcroft	d**n@g**m	2
Stefaan Verwimp	5**p@u**m	1

Committer Domains (Top 20 + Academic)

chifley.ace.uq.edu.au: 1 cl5n010.ib0.hpc.qut.edu.au: 1 howard.ace.uq.edu.au: 1 page.ace.uq.edu.au: 1 cl5n005.ib0.hpc.qut.edu.au: 1 microba.com: 1 uq.edu.au: 1 hdr.qut.edu.au: 1 uqconnect.edu.au: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 13
Total pull requests: 48
Average time to close issues: 7 months
Average time to close pull requests: 11 days
Total issue authors: 5
Total pull request authors: 4
Average comments per issue: 3.08
Average comments per pull request: 0.27
Merged pull requests: 30
Bot issues: 0
Bot pull requests: 17

Past Year

Issues: 4
Pull requests: 1
Average time to close issues: about 14 hours
Average time to close pull requests: N/A
Issue authors: 2
Pull request authors: 1
Average comments per issue: 2.25
Average comments per pull request: 1.0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

rhysnewell (4)
AroneyS (4)
jianshu93 (3)
rwolfe45 (1)

Pull Request Authors

rhysnewell (24)
dependabot[bot] (17)
wwood (7)
StefaanVerwimp (1)

Top Labels

Issue Labels

bug (3) enhancement (2) help wanted (1)

Pull Request Labels

dependencies (17)

Packages

Total packages: 2
Total downloads:
- cargo 3,279 total

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 0
(may contain duplicates)
Total versions: 2
Total maintainers: 1

crates.io: lorikeet-rs

Strain resolver for metagenomics

Homepage: https://rhysnewell.github.io/Lorikeet/
Documentation: https://docs.rs/lorikeet-rs/
License: GPL-3.0
Latest release: 0.3.0
published about 6 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 1,836 Total

Rankings

Stargazers count: 15.7%

Forks count: 16.0%

Dependent repos count: 29.3%

Average: 33.0%

Dependent packages count: 33.8%

Downloads: 70.0%

Maintainers (1)

rhysnewell

Last synced: 7 months ago

crates.io: lorikeet-genome

Strain resolver and variant caller via local reassembly for metagenomics

Homepage: https://rhysnewell.github.io/Lorikeet/
Documentation: https://docs.rs/lorikeet-genome/
License: GPL-3.0
Latest release: 0.8.2
published about 2 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 1,443 Total

Rankings

Stargazers count: 16.3%

Forks count: 16.9%

Dependent repos count: 30.7%

Dependent packages count: 36.2%

Average: 39.7%

Downloads: 98.4%

Maintainers (1)

rhysnewell

Last synced: 7 months ago

Dependencies

.github/workflows/deploy-docs.yaml actions

actions-rs/toolchain v1 composite
actions/checkout v2 composite
crazy-max/ghaction-github-pages v3.0.0 composite
docker://pandoc/core 2.9 composite

.github/workflows/release-lorikeet.yml actions

actions/checkout main composite
actions/upload-artifact v2 composite
marvinpinto/action-automatic-releases latest composite
master-atul/tar-action v1.0.2 composite
rhysnewell/rust-cargo-musl-action v0.1.20 composite

.github/workflows/test-lorikeet.yml actions

actions/checkout v2 composite
conda-incubator/setup-miniconda v2 composite

Cargo.toml cargo

assert_cli 0.6.* development
ansi_term 0.12.1
approx 0.5.0
bio 0.41.0
bio-types 0.13.0
bird_tool_utils-man ^0.4
bstr ^0.2.17
clap ^3
clap_complete ^3
compare 0.1.0
enum-ordinalize ^3.1
env_logger 0.6
finch 0.4.3
gkl ^0.1.1
glob ^0.3
hashlink ^0.7
hts-sys 2.0.3
indexmap ^1.7
indicatif ^0.17.1
itertools ^0.8
lazy_static ^1.3
libm 0.2.1
log ^0.4
mathru 0.9.1
multimap 0.8.3
ndarray ^0.15.3
ndarray-npy ^0.8.0
needletail ^0.4.1
num 0.4.0
openssl ^0.10
openssl-sys ^0.9
ordered-float 1
partitions ^0.2
petgraph ^0.6.0
pyo3 ^0.17
rand 0.6
rayon ^1.5.1
roff ^0.2
rust-htslib 0.39.*
scoped_threadpool ^0.1.9
serde ^1
serde_derive ^1
statrs 0.13
strum ^0.17.1
strum_macros ^0.17.1
tempdir ^0.3
tempfile ^3
term 0.7.0

lorikeet-genome

Science Score: 77.0%

Repository

Basic Info

Statistics

Metadata Files

README.md

Lorikeet

Documentation

Quick Start

Installation

Usage

Shell completion

License

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: lorikeet-rs

Rankings

Maintainers (1)

crates.io: lorikeet-genome

Rankings

Maintainers (1)

Dependencies