Metagenomics_for_IgA

GitHub repository for the project "Metagenomic analysis to identify gene clusters associated with IgA production"

Walkthrough for creating a custom database:

Required folder structure for creating custom database

MIDAS2 main folder

• Default MIDAS2 files and folders

• Scripts

• tests

  • genomes
    • cleaned_imports
      • folders that contain genomes (species_id/genome_id/genome_id.fa)
    • genomes.tsv
  • reads
  • build_midasDB.sh
  • midas_analysis.sh

• Download and unpack custom genomes in 'MIDAS2/tests/genomes' folder.

tar -xvf iMGMC-mMAGs-dereplicated_genomes.tar

• After unpacking the genomes we suggest that you change these folder names as well as the genome .fa file names in these folders.

• This is because of two reasons: 1) MIDAS gives an error when genome folder names are longer than certain numbers of characters. 2) If the genome name contains dots ".", this could create an error.

  • We changed the folder and the genome names using Scripts/folder-setup.sh script.

  • Make sure you move all genome folders in MIDAS2/tests/genomes/cleaned_imports

    • genomes.tsv file should be in the upper directory (MIDAS2/tests/genomes/).
    • Make sure to change the necessary directory names.

  • run bash build_midasDB.sh 20