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Open Source Science

https://github.com/a-slide/metacompore

Metacompore is a snakemake pipeline running multiple RNA modifications detection tools for nanopore directRNA sequencing

https://github.com/a-slide/metacompore

Science Score: 59.0%

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 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 2 committers (50.0%) from academic institutions
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    Institutional organization owner
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    Scientific vocabulary similarity
    Low similarity (12.5%) to scientific vocabulary
Last synced: 7 months ago · JSON representation

Repository

Metacompore is a snakemake pipeline running multiple RNA modifications detection tools for nanopore directRNA sequencing

Basic Info
  • Host: GitHub
  • Owner: a-slide
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 1.15 MB
Statistics
  • Stars: 9
  • Watchers: 2
  • Forks: 2
  • Open Issues: 0
  • Releases: 8
Created over 5 years ago · Last pushed almost 5 years ago
Metadata Files
Readme Contributing License Code of conduct

README.md

MetaCompore v0.1.3

Snakemake DOI

Metacompore is a snakemake pipeline running multiple RNA modifications detection tools for nanopore directRNA sequencing

At the moment MetaCompore supports the following tools: * NanoCompore v1.03 :https://github.com/tleonardi/nanocompore/ * Epinano v1.02: https://github.com/enovoa/EpiNano * Eligos2 v2.0.0: https://gitlab.com/piroonj/eligos2 * Tombo v1.5.1: https://github.com/nanoporetech/tombo * MINES: https://github.com/YeoLab/MINES * differrnanoporeDRS: https://github.com/bartongroup/differrnanoporeDRS

Authors

  • Adrien Leger (@a-slide)
  • Tommaso Leonardi (@tleonardi)

Usage

Step 1: Obtain a copy of this workflow

Clone the last tarball archive of the pipeline to your local system, into the location where you want to perform the data analysis

wget https://github.com/a-slide/MetaCompore/releases/download/0.1.3/MetaCompore.tar.gz tar xzf MetaCompore.tar.gz cd MetaCompore

Step 2: Install dependencies

Singularity

If required, install singularity following the official documentation: https://sylabs.io/guides/3.7/user-guide/quick_start.html

Conda / Mamba

Install miniconda following the official documentation: https://docs.conda.io/en/latest/miniconda.html

you can also install mamba to speed up snakemake installation: https://github.com/mamba-org/mamba

Snakemake

Create a virtual environment containing snakemake with conda conda env create -f environment.yaml

You can also use mamba which will give you the same result, but much faster

mamba env create -f environment.yaml

Step 3: Configure the workflow

Configure the workflow according to your needs by editing the files config.yaml to configure the workflow execution

nano config.yaml

Edit the samples.tsv to specify your sample setup and fast5 source files

nano samples.tsv

Step 4: Execute workflow

Local Mode

Activate the conda environment:

conda activate snakemake snakemake --use-singularity -j 4

LSF cluster Mode

Set an LSF cluster profile https://github.com/Snakemake-Profiles/lsf

Edit the lsf rule specific config file lsf.yaml

Disclaimer

Please be aware that MetaCompore is a research package that is still under development.

It was tested under Linux Ubuntu 16.04 and in an HPC environment running under Red Hat Enterprise 7.1.

Thank you

citation

Adrien Leger & Tommaso Leonardi. (2021, April 28). MetaCompore. Zenodo. http://doi.org/10.5281/zenodo.4726171

licence

MIT (https://mit-license.org/)

Copyright © 2020 Adrien Leger

Authors

  • Adrien Leger / contact@adrienleger.com / https://adrienleger.com

Owner

  • Name: Adrien Leger
  • Login: a-slide
  • Kind: user
  • Location: Oxford, UK
  • Company: @nanoporetech

Research scientist at Oxford Nanopore Technologies

GitHub Events

Total
Last Year

Committers

Last synced: 12 months ago

All Time
  • Total Commits: 30
  • Total Committers: 2
  • Avg Commits per committer: 15.0
  • Development Distribution Score (DDS): 0.067
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
a-slide a****g@e****k 28
Tommaso Leonardi t****m@i****z 2
Committer Domains (Top 20 + Academic)
itm6.xyz: 1 ebi.ac.uk: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 0
  • Total pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 4 days
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
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  • tleonardi (1)
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