NGLess

NGLess: NGS with less work

https://github.com/ngless-toolkit/ngless

Science Score: 75.0%

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
Found .zenodo.json file
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DOI references
Found 6 DOI reference(s) in README
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Academic publication links
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Committers with academic emails
2 of 13 committers (15.4%) from academic institutions
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Institutional organization owner
Organization ngless-toolkit has institutional domain (ngless.embl.de)
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (12.6%) to scientific vocabulary

Keywords

bioinformatics bioinformatics-pipeline bwa fastq fastq-format genomics haskell haskell-language metagenomics next-generation-sequencing ngs samtools science

Last synced: 4 months ago · JSON representation ·

Repository

NGLess: NGS with less work

Basic Info

Host: GitHub
Owner: ngless-toolkit
License: other
Language: Haskell
Default Branch: main
Homepage: https://ngless.embl.de
Size: 14.1 MB

Statistics

Stars: 151
Watchers: 10
Forks: 25
Open Issues: 35
Releases: 21

Topics

bioinformatics bioinformatics-pipeline bwa fastq fastq-format genomics haskell haskell-language metagenomics next-generation-sequencing ngs samtools science

Created about 13 years ago · Last pushed 10 months ago

Metadata Files

Readme Changelog Contributing License Citation Authors

README.md

NGLess: NGS Processing with Less Work

Ngless is a domain-specific language for NGS (next-generation sequencing data) processing.

For questions and discussions, please use the NGLess mailing list.

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

NGLess cartoon

Example

ngless "1.5"
input = fastq(['ctrl1.fq','ctrl2.fq','stim1.fq','stim2.fq'])
input = preprocess(input) using |read|:
    read = read[5:]
    read = substrim(read, min_quality=26)
    if len(read) < 31:
        discard

mapped = map(input,
                reference='hg19')
write(count(mapped, features=['gene']),
        ofile='gene_counts.csv',
        format={csv})

For more information, check the docs. We also have a YouTube tutorial on how to use NGLess and SemiBin together (but you can learn to use NGLess independently of SemiBin).

Installing

See the install documentation for more information.

Bioconda

The recommended way to install NGLess is through bioconda:

conda install -c bioconda ngless

Docker

Alternatively, a docker container with NGLess is available at docker hub:

docker run -v $PWD:/workdir -w /workdir -it nglesstoolkit/ngless:1.5.0 ngless --version

Adapt the mount flags (-v) as needed.

Linux

You can download a statically linked version of NGless 1.5.0

This should work across a wide range of Linux versions (please report any issues you encounter):

curl -L -O https://github.com/ngless-toolkit/ngless/releases/download/v1.5.0/NGLess-v1.5.0-Linux-static-full
chmod +x NGLess-v1.5.0-Linux-static-full
./NGLess-v1.5.0-Linux-static-full

This downloaded file bundles bwa, samtools and megahit (also statically linked).

From Source

Installing/compiling from source is also possible. Clone https://github.com/ngless-toolkit/ngless

Dependencies

The simplest way to get an environment with all the dependencies is to use conda:

conda create -n ngless
conda activate ngless
conda config --add channels conda-forge
conda install stack cairo bzip2 gmp zlib perl wget xz pkg-config make

You should have gcc installed (or another C-compiler).

The following sequence of commands should download and build the software

git clone https://github.com/ngless-toolkit/ngless
cd ngless
stack setup
make

To install, you can use the following command (replace <PREFIX> with the directory where you wish to install, default is /usr/local):

make make

Running Sample Test Scripts on Local Machine

For developers who have successfully compiled and installed NGless, running the test scripts in the tests folder would be the next line of action to have the output of sample test cases.

cd tests

Once in the tests directory, select any of the test folders to run NGless.

For example, here we would run the regression-fqgz test:

cd regression-fqgz
ngless ungzip.ngl

After running this script open the newly generated folder ungzip.ngl.output_ngless and view the template in the index.html file.

For developers who have done this much more datasets for testing purposes can be referenced and used by reading these documentation links: Human Gut Metagenomics Functional & Taxonomic Profiling Ocean Metagenomics Functional Profiling Ocean Metagenomics Assembly and Gene Prediction

More information

Authors

Luis Pedro Coelho (email: luispedro@big-data-biology.org) (on twitter: @luispedrocoelho)
Paulo Monteiro
Renato Alves
Ana Teresa Freitas
Peer Bork

Owner

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

Website: https://ngless.embl.de
Repositories: 8
Profile: https://github.com/ngless-toolkit

Projects around NGLess

Citation (CITATION.cff)

cff-version: 1.1.0
message: If you use this software, please cite it as below.
title: 'NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific
  language'
authors:
- family-names: Coelho
  given-names: Luis Pedro
  orcid: https://orcid.org/0000-0002-9280-7885
- family-names: Alves
  given-names: Renato
  orcid: null
- family-names: Monteiro
  given-names: Paulo
  orcid: null
- family-names: Huerta-Cepas
  given-names: Jaime
  orcid: null
- family-names: Freitas
  given-names: Ana Teresa
  orcid: null
- family-names: Bork
  given-names: Peer
  orcid: null
doi: 10.1186/s40168-019-0684-8
date-released: 2019-12-1
version: 1.3.0

GitHub Events

Total

Watch event: 7
Push event: 1
Fork event: 1

Last Year

Watch event: 7
Push event: 1
Fork event: 1

Committers

Last synced: 8 months ago

All Time

Total Commits: 2,438
Total Committers: 13
Avg Commits per committer: 187.538
Development Distribution Score (DDS): 0.264

Past Year

Commits: 6
Committers: 1
Avg Commits per committer: 6.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Luis Pedro Coelho	l**s@l**g	1,794
Paulo Monteiro	p**m@g**m	207
Renato Alves	a**c@g**m	193
Paulo Monteiro	p**m@k**t	168
Paulo Monteiro	p**o@i**t	64
Sajjal Nair	n**l@g**m	2
Michael Kuhn	m**n@e**e	2
glazek	a**k@e**e	2
Paulo Ricardo Monteiro	m**s@p**e	2
psj1997	1**9@q**m	1
Vedanth Ramji	8****i	1
The Gitter Badger	b**r@g**m	1
Paulo Ricardo Ribeiro Monteiro	i**2@n**t	1

Committer Domains (Top 20 + Academic)

embl.de: 2 nexus.rnl.ist.utl.pt: 1 gitter.im: 1 qq.com: 1 paulos-mbp.home: 1 ist.utl.pt: 1 kdbio.inesc-id.pt: 1 luispedro.org: 1

Issues and Pull Requests

Last synced: 5 months ago

All Time

Total issues: 88
Total pull requests: 12
Average time to close issues: 7 months
Average time to close pull requests: 6 days
Total issue authors: 25
Total pull request authors: 5
Average comments per issue: 2.02
Average comments per pull request: 1.5
Merged pull requests: 11
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

View more stats

Top Authors

Issue Authors

unode (44)
luispedro (11)
uloeber (4)
nairsajjal (3)
mkuhn (3)
ycl6 (3)
liuxianghui (2)
kubu4 (1)
AlessioMilanese (1)
rekado (1)
sternenseemann (1)
kunstner (1)
chodarq (1)
ghost (1)
jakob-wirbel (1)

Pull Request Authors

unode (7)
nairsajjal (2)
mkuhn (1)
Vedanth-Ramji (1)
psj1997 (1)

Top Labels

Issue Labels

enhancement (24) bug (10) better error message (8) help wanted (7) good first issue (5) performance (4) documentation (3) question (1)

Pull Request Labels

Packages

Total packages: 2
Total downloads:
- hackage 470 total

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 0
(may contain duplicates)
Total versions: 30
Total maintainers: 1

proxy.golang.org: github.com/ngless-toolkit/ngless

Documentation: https://pkg.go.dev/github.com/ngless-toolkit/ngless#section-documentation
License: other
Latest release: v1.5.0
published over 3 years ago

Versions: 25
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.4%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 5 months ago

hackage.haskell.org: NGLess

NGLess implements a domain-specific language for processing next generation data, particularly metagenomics.

Homepage: https://github.com/ngless-toolkit/ngless#readme
License: MIT
Latest release: 1.5.0
published over 3 years ago

Versions: 5
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 470 Total

Rankings

Stargazers count: 6.1%

Forks count: 6.8%

Dependent packages count: 12.2%

Average: 35.0%

Dependent repos count: 55.1%

Downloads: 94.8%

Maintainers (1)

luispedro

Last synced: 5 months ago

Dependencies

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.github/workflows/build_static_embedded_nix.yml actions

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.github/workflows/build_w_nix.yml actions

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