pATLAS-db-creation

This repository is a wrapper for the creation of pATLAs database. It will not make the pATLAS service run but will create the necessary files to construct pATLAS, including:

• JSON file for the initial load of pATLAS (devel session) - results/MASHix/<database_name>/results/import_to_vivagraph.json.
• sql file to migrate the database between machines - results/sql_file/<database_name>_final.sql.
• JSON files that are used to populate the drop down menus of pATLAS - results/sql_file/*.json and results/MASHix/taxa_tree.json.
• Fasta file with all the sequences available in pATLAS - resuts/MASHix/<database_name>/master_fasta_<database_name>.fas
  • indexes for bowtie2 and samtools (required by pATLASflow) - results/samtools_indexes/*.fai
  • index for mash (required by pATLASflow) - results/bowtie_indexes/bowtie2_index*
  • json file used by pATLASflow and FlowCraft to fetch a dictionary of plasmid sizes - results/MASHix/<database_name>/length_<database_name>.json.

Link to pATLAS source code.

Workflow

This nextflow script intends to handle everything that is required to create pATLas database, from download of sequences from NCBI ftp to the final PostgreSQL database, with the sequences for all plasmids, metadata, annotations and other sql tables required for pATLAS REST API (requests of sequences, metadata or even to display results using a POST from an external pipeline). Here is a description of the steps that this script handles.

Usage

--help - prints this help
--db_name - A string with the database name to create and dump
--abricateDatabases - A list of databases to use by abricate. Default: ['resfinder', 'card', 'plasmidfinder', 'vfdb', 'virulencefinder']
--ncbi_ftp - The link to the plasmid sequences from ncbi refseq. Default: 'ftp://ftp.ncbi.nlm.nih.gov/refseq/release/plasmid/plasmid.*.1.genomic.fna.gz'
--abricateId - The identity percentage for blast searches (abricate). Default: 90
--abricateCov - The coverage percentage for blast searches (abricate). Default: 80
--sequencesRemove - A variable that allows to only generate the fasta file and stop the script. Default: false