Directory Structure - AndreaRP/METAGENOMICS GitHub Wiki

Here we detail the directory structure that pikaVir creates:

• References
  Databases the workflow will use to run the analysis. You can consult a detailed guide to generate them in the References section in this wiki. The path to each organism database needs to be specified in the configuration file as follows:
  - Human -> hostDB
  - Virus -> virDB
  - Bacteria -> bacDB
  - Fungi -> fungiDB
  - Protozoa -> protozoaDB
  - Invertebrate -> invertebrateDB

• [Analysis] (https://github.com/AndreaRP/METAGENOMICS/wiki/Directory-Structure#--analysisdir)
  All the files of the analysis will be saved inside this folder. It needs to be specified in the configuration file as analysisDir.

• [Results] ()
  This directory will contain the results in html format. It needs to be specified in the configuration file as resultsDir.

---

- analysisDir/

- 00-reads/

 - sampleName1_*_R1_*._fastq.gz
 - sampleName1_*_R2_*._fastq.gz
 - ...
 - sampleNameN_*_R1_*._fastq.gz
 - sampleNameN_*_R2_*._fastq.gz

- 01-fastqc/

  - sampleName1/
  - ...
  - sampleNameN/

- 02-preprocessing/

  - sampleName1/
  - ...
  - sampleNameN/

- 03-preproQC/

  - sampleName1/
  - ...
  - sampleNameN/

- 04-noHost/

  - sampleName1/
  - ...
  - sampleNameN/

- 05-bacteria/

  - sampleName1/
      - blast/
      - contigs/
      - coverage/
      - reads/
  - ...
  - sampleNameN/
      - blast/
      - contigs/
      - coverage/
      - reads/

- 06-virus/

  - sampleName1/
    - blast/
    - contigs/
    - coverage/
    - reads/
  - ...
  - sampleNameN/
    - blast/
    - contigs/
    - coverage/
    - reads/

- 07-fungi/

  - sampleName1/
    - blast/
    - contigs/
    - coverage/
    - reads/
  - ...
  - sampleNameN/
    - blast/
    - contigs/
    - coverage/
    - reads/

- 08-protozoa/

  - sampleName1/
    - blast/
    - contigs/
    - coverage/
    - reads/
  - ...
  - sampleNameN/
    - blast/
    - contigs/
    - coverage/
    - reads/

- 09-invertebrate/

  - sampleName1/
    - blast/
    - contigs/
    - coverage/
    - reads/
  - ...
  - sampleNameN/
    - blast/
    - contigs/
    - coverage/
    - reads/

- 99-stats/

  - sampleName1/
    - sampleName1_prePro_R1_fastqc
    - sampleName1_prePro_R2_fastqc
    - sampleName1_trimmed_R1_fastqc
    - sampleName1_trimmed_R2_fastqc
  - ...
  - sampleNameN/
    - sampleNameN_prePro_R1_fastqc
    - sampleNameN_prePro_R2_fastqc
    - sampleNameN_trimmed_R1_fastqc
    - sampleNameN_trimmed_R2_fastqc

- REFERENCES/

- HUMAN_GENOME_REFERENCE/

 - WG/
    - bwt2/
        - hg38.AnalysisSet.1.bt2  
        - ...  
        - hg38.AnalysisSet.n.bt2  
        - hg38.AnalysisSet.rev.1.bt2 
        - ...   
        - hg38.AnalysisSet.rev.n.bt2  

- BACTERIA_GENOME_REFERENCE/

 - BLAST/
   - blastn/
       - bacteria_blastn.nhr
       - bacteria_blastn.nin
       - bacteria_blastn.nog
       - bacteria_blastn.nsd
       - bacteria_blastn.nsi
       - bacteria_blastn.nsq   
 - 16S/
   - bwt2/
       - 16S.1.bt2
       - ...
       - 16S.n.bt2
       - 16S.rev.1.bt2
       - ...
       - 16S.rev.n.bt2 
 - WG/
   - genome_length.txt
   - bwt2/
       - WG.1.bt2
       - ...
       - WG.n.bt2
       - WG.rev.1.bt2
       - ...
       - WG.rev.n.bt2   

- VIRUS_GENOME_REFERENCE/

 - BLAST/
   - blastn/
       - VIRUS_blastn.nhr
       - VIRUS_blastn.nin
       - VIRUS_blastn.nog
       - VIRUS_blastn.nsd
       - VIRUS_blastn.nsi
       - VIRUS_blastn.nsq   
   - blastx/
       - VIRUS_blastx.phr
       - VIRUS_blastx.pin
       - VIRUS_blastx.pog
       - VIRUS_blastx.psd
       - VIRUS_blastx.psi
       - VIRUS_blastx.psq  
 - WG/
   - genome_length.txt
   - bwt2/
       - virus_all.1.bt2
       - ...
       - virus_all.n.bt2
       - virus_all.rev.1.bt2
       - ...
       - virus_all.rev.n.bt2  

- FUNGI_GENOME_REFERENCE/

 - BLAST/
   - blastn/
       - FUNGI_blastn.nhr
       - FUNGI_blastn.nin
       - FUNGI_blastn.nog
       - FUNGI_blastn.nsd
       - FUNGI_blastn.nsi
       - FUNGI_blastn.nsq    
 - ITS/
   - bwt2/
       - ITS_all.1.bt2
       - ...
       - ITS_all.n.bt2
       - ITS_all.rev.1.bt2
       - ...
       - ITS_all.rev.n.bt2 
 - WG/
   - genome_length.txt
   - bwt2/
       - fungi_all.1.bt2
       - ...
       - fungi_all.n.bt2
       - fungi_all.rev.1.bt2
       - ...
       - fungi_all.rev.n.bt2  

- INVERTEBRATE_GENOME_REFERENCE/

 - BLAST/
   - blastn/
       - INVERTEBRATE_blastn.nhr
       - INVERTEBRATE_blastn.nin
       - INVERTEBRATE_blastn.nog
       - INVERTEBRATE_blastn.nsd
       - INVERTEBRATE_blastn.nsi
       - INVERTEBRATE_blastn.nsq   
 - WG/
   - genome_length.txt
   - bwt2/
       - invertebrate_all.1.bt2
       - ...
       - invertebrate_all.n.bt2
       - invertebrate_all.rev.1.bt2
       - ...
       - invertebrate_all.rev.n.bt2  

- PROTOZOA_GENOME_REFERENCE/

 - BLAST/
   - blastn/
       - PROTOZOA_blastn.nhr
       - PROTOZOA_blastn.nin
       - PROTOZOA_blastn.nog
       - PROTOZOA_blastn.nsd
       - PROTOZOA_blastn.nsi
       - PROTOZOA_blastn.nsq   
 - WG/
   - genome_length.txt
   - bwt2/
       - protozoa_all.1.bt2
       - ...
       - protozoa_all.n.bt2
       - protozoa_all.rev.1.bt2
       - ...
       - protozoa_all.rev.n.bt2