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ufcg

UFCG: Universal Fungal Core Genes

https://github.com/steineggerlab/ufcg

Science Score: 57.0%

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
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.0%) to scientific vocabulary

Keywords

bioinformatics fungi genomics marker-gene-analysis phylogenetics
Last synced: 4 months ago · JSON representation ·

Repository

UFCG: Universal Fungal Core Genes

Basic Info
Statistics
  • Stars: 32
  • Watchers: 3
  • Forks: 0
  • Open Issues: 21
  • Releases: 7
Topics
bioinformatics fungi genomics marker-gene-analysis phylogenetics
Created about 4 years ago · Last pushed 11 months ago
Metadata Files
Readme License Citation

README.md

UFCG pipeline

Build License Bioconda Docker

UFCG pipeline provides methods for a genome-wide taxonomic profiling and annotation of your own biological sequences of Fungi. * Homepage * Publication

How to cite

Kim, D., Gilchrist, C.L.M., Chun, J. & Steinegger, M. (2023) UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi. Nucleic Acids Research, 51(D1), D777-D784, doi:10.1093/nar/gkac894.

Installation

Quick start with conda

~~~bash conda install -y ufcg # conda-libmamba-solver recommended ufcg download -t minimum ufcg -h ~~~

Quick start with docker

~~~bash docker pull endix1029/ufcg:latest docker run -it endix1029/ufcg:latest ufcg -h ~~~

Build from source

Build requirements

  • Java 8 or higher
  • Maven 3.9.4 or higher

Build

~~~bash git clone https://github.com/steineggerlab/ufcg.git cd ufcg mvn clean package appassembler:assemble ./target/bin/ufcg -h ~~~

Runtime requirements

  • Java 8 or higher
  • profile - AUGUSTUS v3.5.0 or higher
  • profile - MMseqs2 v13 or higher
  • tree - MAFFT v7.310 or higher
  • tree - IQ-TREE v2.0.3 or higher

Modules

profile

UFCG profile extracts marker gene sequences from your own Fungal biological data, including genome sequences, transcriptome sequences, and proteome sequences. * Interactive mode ~~~bash ufcg profile -u ~~~ * I/O mode ~~~bash ufcg profile -i -o [OPTIONS] ~~~

tree

UFCG tree reconstructs the phylogenetic relationship of the set of marker gene profiles. ~~~bash ufcg tree -i -o [OPTIONS] ~~~

train

UFCG train generates sequence model of your own fungal marker gene, even from a small set of seed sequences. ~~~bash ufcg train -i -g -o [OPTIONS] ~~~

align

UFCG align conducts multiple sequence alignment of the genes from the set of marker gene profiles. ~~~bash ufcg align -i -o [OPTIONS] ~~~

Owner

  • Name: Steinegger Lab
  • Login: steineggerlab
  • Kind: organization
  • Email: martin.steinegger@snu.ac.kr
  • Location: Korea, South

Steinegger Lab Github repositories

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Kim"
  given-names: "Dongwook"
  orcid: "https://orcid.org/0000-0001-7386-3163"
- family-names: "Gilchrist"
  given-names: "Cameron"
  orcid: "https://orcid.org/0000-0001-7798-427X"
- family-names: "Chun"
  given-names: "Jongsik"
  orcid: "https://orcid.org/0000-0003-3385-5171"
- family-names: "Steinegger"
  given-names: "Martin"
  orcid: "https://orcid.org/0000-0001-8781-9753"
title: "UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi"
version: 1.0.2
doi: 10.1093/nar/gkac894
preferred-citation:
  type: article
  authors:
  - family-names: "Kim"
    given-names: "Dongwook"
    orcid: "https://orcid.org/0000-0001-7386-3163"
  - family-names: "Gilchrist"
    given-names: "Cameron"
    orcid: "https://orcid.org/0000-0001-7798-427X"
  - family-names: "Chun"
    given-names: "Jongsik"
    orcid: "https://orcid.org/0000-0003-3385-5171"
  - family-names: "Steinegger"
    given-names: "Martin"
    orcid: "https://orcid.org/0000-0001-8781-9753"
  doi: 10.1093/nar/gkac894
  journal: "Nucleic Acids Research"
  title: "UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi"
  issue: 51
  volume: D1
  start: D777
  end: D784
  year: 2023

GitHub Events

Total
  • Issues event: 6
  • Watch event: 3
  • Delete event: 1
  • Issue comment event: 11
  • Push event: 2
  • Pull request event: 2
  • Create event: 1
Last Year
  • Issues event: 6
  • Watch event: 3
  • Delete event: 1
  • Issue comment event: 11
  • Push event: 2
  • Pull request event: 2
  • Create event: 1

Issues and Pull Requests

Last synced: 9 months ago

All Time
  • Total issues: 36
  • Total pull requests: 3
  • Average time to close issues: 24 days
  • Average time to close pull requests: 1 minute
  • Total issue authors: 22
  • Total pull request authors: 1
  • Average comments per issue: 3.06
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 3
Past Year
  • Issues: 9
  • Pull requests: 1
  • Average time to close issues: about 12 hours
  • Average time to close pull requests: 1 minute
  • Issue authors: 7
  • Pull request authors: 1
  • Average comments per issue: 1.33
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 1
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Pull Request Authors
  • dependabot[bot] (4)
Top Labels
Issue Labels
bug (5) enhancement (3) invalid (1) good first issue (1) wontfix (1) question (1)
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Dependencies

.github/workflows/maven-build.yml actions
  • actions/checkout v3 composite
  • actions/setup-java v3 composite
Dockerfile docker
  • ubuntu focal build
pom.xml maven
  • commons-lang:commons-lang 2.6 compile
  • com.googlecode.json-simple:json-simple 1.1
  • commons-cli:commons-cli 1.5.0
  • commons-io:commons-io 2.11.0
  • org.json:json 20220924
  • lumberjack-mismatch:lumberjack-mismatch 1.0 system