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assembly_finder

snakemake-powered cli to download genomes using NCBI datasets

https://github.com/metagenlab/assembly_finder

Science Score: 67.0%

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  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 9 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (11.0%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

snakemake-powered cli to download genomes using NCBI datasets

Basic Info
Statistics
  • Stars: 14
  • Watchers: 4
  • Forks: 0
  • Open Issues: 1
  • Releases: 20
Created almost 7 years ago · Last pushed 11 months ago
Metadata Files
Readme License Citation

README.md

assembly_finder

tests docs docker

snaketool license version downloads

DOI paper

assembly_finder is a Snakemake CLI wrapper for NCBI datasets, written with Snaketool, for easy genome assembly downloads.

:zap: Quick start

Installation

Conda

sh conda create -n assembly_finder -c bioconda assembly_finder

Apptainer

sh apptainer pull docker://ghcr.io/metagenlab/assembly_finder:latest

Usage

sh assembly_finder -i staphylococcus_aureus --reference

Output

sh 📂staphylococcus_aureus ┣ 📂download ┃ ┣ 📂GCF_000013425.1 ┃ ┃ ┗ 📜GCF_000013425.1_ASM1342v1_genomic.fna.gz ┃ ┗ 📜.snakemake_timestamp ┣ 📂logs ┃ ┣ 📂taxons ┃ ┃ ┗ 📜staphylococcus_aureus.log ┃ ┣ 📜archive.log ┃ ┣ 📜lineage.log ┃ ┣ 📜rsync.log ┃ ┗ 📜unzip.log ┣ 📜archive.zip ┣ 📜assembly_finder.log ┣ 📜assembly_summary.tsv ┣ 📜config.yaml ┣ 📜sequence_report.tsv ┗ 📜taxonomy.tsv

:books: Documentation

You can find more information on assembly_finder's inputs, outputs and example commands in the documentation

:scroll: Help

`assembly_finder -h`

Citation

Please consider citing assembly_finder if you use it in your work.

Farid Chaabane, Trestan Pillonel, Claire Bertelli, MeSS and assembly_finder: A toolkit for in silico metagenomic sample generation, Bioinformatics, 2024;, btae760, https://doi.org/10.1093/bioinformatics/btae760

BibTeX @article{chaabane_mess_2024, title = {MeSS and assembly_finder: A toolkit for in silico metagenomic sample generation}, issn = {1367-4811}, url = {https://doi.org/10.1093/bioinformatics/btae760}, doi = {10.1093/bioinformatics/btae760}, journal = {Bioinformatics}, author = {Chaabane, Farid and Pillonel, Trestan and Bertelli, Claire}, month = dec, year = {2024}, pages = {btae760}, }

Owner

  • Name: metagenlab
  • Login: metagenlab
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.2.0
title: "assembly_finder: download genomes using NCBI datasets"
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Farid
    family-names: Chaabane
    email: farid.chaabane@chuv.ch
    affiliation: >-
      Institute of Microbiology, Lausanne University
      Hospital and University of Lausanne, Lausanne,
      Switzerland
    orcid: 'https://orcid.org/0009-0007-9322-1281'
  - given-names: Trestan
    family-names: Pillonel
    email: trestan.pillonel@chuv.ch
    affiliation: >-
      Institute of Microbiology, Lausanne University
      Hospital and University of Lausanne, Lausanne,
      Switzerland
    orcid: 'https://orcid.org/0000-0003-0550-8981'
  - given-names: Claire
    family-names: Bertelli
    email: claire.bertelli@chuv.ch
    affiliation: >-
      Institute of Microbiology, Lausanne University
      Hospital and University of Lausanne, Lausanne,
      Switzerland
    orcid: 'https://orcid.org/0000-0003-0550-8981'
identifiers:
  - type: doi
    value: 10.5281/zenodo.13985668
    description: zenodo
repository-code: 'https://github.com/metagenlab/assembly_finder'
url: 'https://metagenlab.github.io/assembly_finder/'
abstract: >-
  Snakemake-powered cli to download genomes using NCBI
  datasets 
license: MIT
preferred-citation:
  type: article
  authors:
    - given-names: Farid
      family-names: Chaabane
    - given-names: Trestan
      family-names: Pillonel
    - given-names: Claire
      family-names: Bertelli
  doi: "10.1093/bioinformatics/btae760"
  journal: "Bioinformatics"
  title: "MeSS and assembly_finder: A toolkit for in silico metagenomic sample generation"
  year: 2024
  url: "https://doi.org/10.1093/bioinformatics/btae760"

GitHub Events

Total
  • Release event: 1
  • Watch event: 1
  • Delete event: 6
  • Push event: 24
  • Pull request event: 10
  • Create event: 8
Last Year
  • Release event: 1
  • Watch event: 1
  • Delete event: 6
  • Push event: 24
  • Pull request event: 10
  • Create event: 8

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 0
  • Total pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: 1 day
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: 1 day
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
Pull Request Authors
  • farchaab (19)
  • njohner (1)
Top Labels
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enhancement (1)

Dependencies

setup.py pypi