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datascout

This repo queries and gather data from different resources which can then be used to run bulk automatised annotation of microbial genomes.The different types of data are: OrthoDB and UniProt orthology data; Rfam (non coding Rna data); Transcriptomic data from ENA

https://github.com/EBI-Metagenomics/datascout

Science Score: 52.0%

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    Organization ebi-metagenomics has institutional domain (www.ebi.ac.uk)
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    Low similarity (7.1%) to scientific vocabulary
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Repository

This repo queries and gather data from different resources which can then be used to run bulk automatised annotation of microbial genomes.The different types of data are: OrthoDB and UniProt orthology data; Rfam (non coding Rna data); Transcriptomic data from ENA

Basic Info
  • Host: GitHub
  • Owner: EBI-Metagenomics
  • License: mit
  • Language: Python
  • Default Branch: master
  • Size: 371 KB
Statistics
  • Stars: 0
  • Watchers: 3
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created almost 2 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

datascout

This repo queries and gather data from different resources which can then be used to run bulk automatised annotation of microbial genomes. The different types of data are: - OrthoDB and UniProt orthology data; - Rfam (non coding Rna data); - Transcriptomic data from ENA - Genome sequence file from ENA

Getting this repo

git clone git@github.com:manuelcarbajo/datascout

Configuration

Refresing environment

This project uses nextflow-24.04.3

Initialising and running the environment

After downloading the datascout repo define a PROJECT_DIR variable (path to datascout git repo). export PROJECTDIR="/path/to/your/Ensembl-datascout" cd ${PROJECTDIR}

Define the configuration of USER/PWD/SERVER/PORT of your mysql ncbitax and rfam DBs in ""${PROJECTDIR}/conf/ncbidb.conf"" and ""${PROJECTDIR}/conf/rfamdb.conf"" following the structure in the template in that same folder: mysql://USER:PWD@mysql-ncbi-SERVER:PORT/ncbitaxonomy_db.

Test the configuration with: nextflow run main.nf -profile slurm,test,singularity Use a comma separated list of genomes to annotate as input
(following the template in ""${PROJECTDIR}/assets/testdata/genomestestlist.csv"")

GENOMENAME TAXID ENAACCESSION
#Example:
toxoplasmagondiiME49,508771,GCA000006565.2
tripanosomacruzi,5693,GCA003719455.1

Define and export the following variables:

export INPUTCSV="/path/to/your/input-file-dir/yourgenomeslist.csv" export OUTPUTPATH="/path/to/your/output-dir/genome_annotations"

export ORTHODBFOLDER="/path/to/your/static-storage-dir/orthodbdir" export ASSEMBLIESDIR="/path/to/your/static-storage-dir/assembliesdir" export ENACSVDIR="/path/to/your/static-storage-dir/enacsvdir" export FASTQDIR="/path/to/your/static-storage-dir/rnafastqdir" export UNIPROTDIR="/path/to/your/static-storage-dir/uniprot_dir"

To run the pipeline execute: nextflow run main.nf --csv_file $INPUT_CSV --outdir $OUTPUT_PATH --orthodb_dir $ORTHODB_FOLDER --assemblies_dir $ASSEMBLIES_DIR --rna_fastq_dir $FASTQ_DIR --uniprot_dir $UNIPROT_DIR --ena_csv_dir $ENA_CSV_DIR -profile slurm

UPDATED - Initialising and running the environment

nextflow run main.nf --samplesheet {SAMPLESHEET} --output {OUTPUTDIR} --max_runs {MAX NO TRANSCRIPTOME RUNS TO DOWNLOAD}

Owner

  • Name: MGnify
  • Login: EBI-Metagenomics
  • Kind: organization
  • Email: metagenomics-help@ebi.ac.uk
  • Location: Genome Campus, UK

MGnify (formerly known as EBImetagenomics) is a free resource for the assembly, analysis, archiving and browsing all types of microbiome derived sequence data

Citation (CITATIONS.md) 

# Ensembl/datascout: Citations

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

## Pipeline tools

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

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Dependencies

modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
subworkflows/nf-core/utils_nextflow_pipeline/meta.yml cpan
subworkflows/nf-core/utils_nfcore_pipeline/meta.yml cpan
subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml cpan
modules/nf-core/fastqc/environment.yml pypi
modules/nf-core/multiqc/environment.yml pypi