PB-metagenomics-tools is a suite of tools for performing metagenomic analyses using HiFi sequencing data. It comprises four pipelines: HiFi-MAG-Pipeline, Taxonomic-Profiling-Diamond-Megan, Taxonomic-Profiling-Minimap-Megan and Taxonomic-Profiling-Sourmash.

Reference:

• Yunjie Tong, Lia M. Hocke and Blaise B. Frederick, Low Frequency Systemic Hemodynamic “Noise” in Resting State BOLD fMRI: Characteristics, Causes, Implications, Mitigation Strategies, and Applications
  Frfontieres in Neuroscience, 13, Article 787 (2019).
  Documentation
  • pb-metagenomics-tools Github page
  • Tutorial for HiFi-MAG-Pipeline
  • Tutorial for Taxonomic-Profiling-Diamond-Megan
  • Tutorial for Taxonomic-Profiling-Minimap-Megan
  • Tutorial for Taxonomic-Profiling-Sourmash
  Important Notes
  • Module Name: pb-metagenomics-tools (see the modules page for more information)
  • Unusual environment variables set
    • PMT_HOME  installation directory
    • PMT_BIN       executable directory
    • PMT_SRC       source code directory
    • PMT_DATA  sample data directory
  Interactive job
  Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

  Allocate an interactive session and run the program. Sample session:

  [user@biowulf]$ sinteractive
  [user@cn3335 ~]$ module load pb-metagenomics-tools 
  [+] Loading singularity  4.0.1  on cn3335
  [+] Loading pb-metagenomics-tools 2.1.0  ...
  [user@cn3335 ~]$ ls $PMT_DATA
  fastani  markers  mash  masks  metadata  mrca_red  msa  pplacer  radii  split  taxonomy  temp
  

  Available executables:

  [user@cn3335 ~]$ ls $PMT_BIN
  Fasta-Make-Long-Seq-Bins.py  GTDBTk-Organize.py          Plot-Figures.py
  Convert-JGI-Coverages.py  Filter-Checkm2-Bins.py       MAG-Summary.py            
  Copy-Final-MAGs.py        Filter-Complete-Contigs.py   Make-Incomplete-Contigs.py 
  [user@cn3335 ~]$ exit
  [user@biowulf ~]$