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ng-meta-profiler

Profiler for metagenomics based on NGLess

https://github.com/ngless-toolkit/ng-meta-profiler

Science Score: 52.0%

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
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    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
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    DOI references
    Found 4 DOI reference(s) in README
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    Academic publication links
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    Institutional organization owner
    Organization ngless-toolkit has institutional domain (ngless.embl.de)
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    Scientific vocabulary similarity
    Low similarity (11.5%) to scientific vocabulary

Keywords

bioinformatics metagenomics microbiome ngless
Last synced: 6 months ago · JSON representation ·

Repository

Profiler for metagenomics based on NGLess

Basic Info
  • Host: GitHub
  • Owner: ngless-toolkit
  • Language: Shell
  • Default Branch: master
  • Homepage: https://ngless.embl.de
  • Size: 32.2 KB
Statistics
  • Stars: 13
  • Watchers: 2
  • Forks: 2
  • Open Issues: 1
  • Releases: 1
Topics
bioinformatics metagenomics microbiome ngless
Created almost 8 years ago · Last pushed about 2 years ago
Metadata Files
Readme Changelog Citation

README.md

NGLESS-PROFILER

https://ngless.embl.de

This is a collection of predefined ngless pipelines for processing shotgun metagenomes.

  1. human-gut.ngl for human gut samples

  2. marine.ngl for marine samples

  3. mouse-gut.ngl for mouse gut samples

  4. dog-gut.ngl for dog gut samples

  5. pig-gut.ngl for pig gut samples

These are predefined, but users are encouraged to adapt them to their specific needs.

Citation

If you are using NG-meta-profiler (or any NGLess-based pipeline), please cite:

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language by Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork, Microbiome (2019) https://doi.org/10.1186/s40168-019-0684-8

INSTALL

You need to

  1. install ngless. The recommended way is through bioconda:

    conda install -c bioconda ngless

Alternatively, see the ngless documentation on how to install it.

  1. copy the profiling scripts to next to where your data lives

USAGE

To use the profiler, select the appropriate script (e.g., human-gut.ngl for human gut samples), put all the FastQ files from the same sample in the same directory (INPUT-DIRECTORY) with the extension .fq.gz or fastq.gz and run:

ngless human-gut.ngl INPUT-DIRECTORY OUTPUT-DIRECTORY

You can use all the ngless command line options to set options. For example, to use 8 cores, use:

ngless --threads=8 human-gut.ngl INPUT-DIRECTORY OUTPUT-DIRECTORY

If you want very verbose output:

ngless --threads=8 --trace human-gut.ngl INPUT-DIRECTORY OUTPUT-DIRECTORY

USAGE WITH DOCKER

We now also provide docker containers containing all required databases on docker hub.

These images can be used directly or through the convenience script ng-meta-profiler.sh. To use ng-meta-profiler.sh simply download the script, decide which profiler to use (human-gut:1.0.0 in the example) and run:

ng-meta-profiler.sh human-gut:1.0.0 INPUT-DIRECTORY OUTPUT-DIRECTORY

which will download and analyse the specified data with the human-gut:1.0.0 profiler.

INPUT and OUTPUT should be absolute paths and INPUT should be a directory containing a metagenome as a set of files named according to the MOCAT format.

RESOURCE REQUIREMENTS

| Profiler | Memory | Disk space | |----------|--------|------------| | Human | 14.7G | 18G | | Mouse | 5.1G | 6.3G | | Dog | 4.5G | 3.5G | | Pig | 10.1G | 17G |

Note too that the first time you run a particular profiler, NGLess will download and index the respective databases. This is likely to take several hours (and this process does not benefit from using multiple threads). This is only necessary once. Afterwards, the index will be reused (this is what is responsible for disk space usage in the table above).

GETTING HELP

Owner

  • Name: NGLess and related utilities
  • Login: ngless-toolkit
  • Kind: organization
  • Email: luispedro@big-data-biology.org

Projects around NGLess

Citation (CITATION.md) 

If you are using NGLess, please cite:

> _NG-meta-profiler: fast processing of metagenomes using NGLess, a
> domain-specific language_ by Luis Pedro Coelho, Renato Alves, Paulo Monteiro,
> Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork, Microbiome (2019)
> [https://doi.org/10.1186/s40168-019-0684-8](https://doi.org/10.1186/s40168-019-0684-8)

GitHub Events

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  • Watch event: 1
Last Year
  • Watch event: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 4
  • Total pull requests: 0
  • Average time to close issues: 4 months
  • Average time to close pull requests: N/A
  • Total issue authors: 4
  • Total pull request authors: 0
  • Average comments per issue: 1.75
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: 1 day
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • 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
  • EorgeKit (1)
  • Sanrrone (1)
  • unode (1)
  • luispedro (1)
Pull Request Authors
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Dependencies

containers/docker-compose.yml docker
  • nglesstoolkit/ng-meta-dog-gut 1.0.0
  • nglesstoolkit/ng-meta-human-gut 1.0.0
  • nglesstoolkit/ng-meta-marine 1.0.0
  • nglesstoolkit/ng-meta-mouse-gut 1.0.0
  • nglesstoolkit/ng-meta-pig-gut 1.0.0
  • nglesstoolkit/ngless 1.0.0