VecTreeID : Taxonomic Identification Pipeline

Created for Neafsey Lab @ Harvard School of Public Health

Maintained by Genomic Center for Infectious Diseases @ Broad Institute of MIT & Harvard

Contact: Jason Travis Mohabir (jmohabir@broadinstitute.org)

Public repository for the amplicon taxonomic identification in the Neafsey lab.

See the README in each corresponding pipeline for usage.

Installation

Install Anaconda3

The online documentation on how to install Anaconda 3 is given here: https://docs.anaconda.com/anaconda/install/linux/

Follow your Operating System specific instructions on how to install Anaconda3

Create conda environment for running the tool

Use the TaxonomyAssignmentPipeline.yml file to create a conda virtual environment

conda env create --file TaxonomyAssignmentPipeline.yml -p /path/to/env/<name-of-environment>/

To activate the conda environment

source activate <name-of-environment>

A detail description on creating a conda environment is given here: https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-from-an-environment-yml-file

Important Note

The version of ete3 used is unable to parse the jplace output from EPA-ng. Users will need to manually update the 'newick.py' file in the conda environment after it has been initially created.

Replace the /lib/python3.10/site-packages/ete3/parser/newick.py file with the `newick.py' file provided.

The development team is working on this issue.

Arguments

 __      __    _______            _____ _____  
 \ \    / /   |__   __|          |_   _|  __ \ 
  \ \  / /__  ___| |_ __ ___  ___  | | | |  | |
   \ \/ / _ \/ __| | '__/ _ \/ _ \ | | | |  | |
    \  /  __/ (__| | | |  __/  __/_| |_| |__| |
     \/ \___|\___|_|_|  \___|\___|_____|_____/ 
                                               
                                               
    [Created on π Day 2023]
    [Authors: Jason Travis Mohabir, Aina Zurita Martinez]
    [Created for Neafsey Lab @ Harvard School of Public Health]
    [Maintained by Genomic Center for Infectious Diseases @ Broad Institute of MIT & Harvard]
    
usage: VecTreeID: Taxonomy Assignment Pipeline for VectorSeq [-h] [--name NAME] --amplicon AMPLICON
                                                             [--dada2_directory DADA2_DIRECTORY]
                                                             [--working_directory WORKING_DIRECTORY]
                                                             [--min_asv_readcount MIN_ASV_READCOUNT]
                                                             [--min_sample_readcount MIN_SAMPLE_READCOUNT]
                                                             [--max_target_seq MAX_TARGET_SEQ]
                                                             [--artefact_cutoff ARTEFACT_CUTOFF] [--min_coverage MIN_COVERAGE]
                                                             [--min_identity MIN_IDENTITY] [--lwr_cutoff LWR_CUTOFF]
                                                             [--max_haplotypes_per_sample MAX_HAPLOTYPES_PER_SAMPLE]
                                                             [--min_abundance_assignment MIN_ABUNDANCE_ASSIGNMENT]
                                                             [--temp_dir TEMP_DIR] [--reference_tree REFERENCE_TREE]
                                                             [--reference_msa REFERENCE_MSA]
                                                             [--reference_database REFERENCE_DATABASE] [--blast_only]
                                                             [--run_blast] [--run_msa] [--run_tree]

options:
  -h, --help            show this help message and exit
  --name NAME           name of batch
  --amplicon AMPLICON   amplicon name
  --dada2_directory DADA2_DIRECTORY
                        DADA2 directory with inputs
  --working_directory WORKING_DIRECTORY
                        working directory
  --min_asv_readcount MIN_ASV_READCOUNT
                        asv total read count threshold
  --min_sample_readcount MIN_SAMPLE_READCOUNT
                        sample total read count threshold
  --max_target_seq MAX_TARGET_SEQ
                        blastn max_target_seq
  --artefact_cutoff ARTEFACT_CUTOFF
                        artefact filter (coverage & identity)
  --min_coverage MIN_COVERAGE
                        percent coverage filter
  --min_identity MIN_IDENTITY
                        percent identity filter
  --lwr_cutoff LWR_CUTOFF
                        Like Weight Ratio cutoff
  --max_haplotypes_per_sample MAX_HAPLOTYPES_PER_SAMPLE
                        maximum number of ASVs for batch-level
  --min_abundance_assignment MIN_ABUNDANCE_ASSIGNMENT
                        minimum ASV read count abundance
  --temp_dir TEMP_DIR   temporary directory
  --reference_tree REFERENCE_TREE
                        reference tree
  --reference_msa REFERENCE_MSA
                        reference msa
  --reference_database REFERENCE_DATABASE
                        reference BLAST database
  --blast_only          only run blastn
  --run_blast           run blast
  --run_msa             run msa
  --run_tree            run tree

(c) 2024 Broad Institute