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

Source: https://github.com/etetoolkit/ete/pull/636

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

```

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[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 [--dada2directory DADA2DIRECTORY] [--workingdirectory WORKINGDIRECTORY] [--minasvreadcount MINASVREADCOUNT] [--minsamplereadcount MINSAMPLEREADCOUNT] [--maxtargetseq MAXTARGETSEQ] [--artefactcutoff ARTEFACTCUTOFF] [--mincoverage MINCOVERAGE] [--minidentity MINIDENTITY] [--lwrcutoff LWRCUTOFF] [--maxhaplotypespersample MAXHAPLOTYPESPERSAMPLE] [--minabundanceassignment MINABUNDANCEASSIGNMENT] [--tempdir TEMPDIR] [--referencetree REFERENCETREE] [--referencemsa REFERENCEMSA] [--referencedatabase REFERENCEDATABASE] [--blastonly] [--runblast] [--runmsa] [--runtree]

options: -h, --help show this help message and exit --name NAME name of batch --amplicon AMPLICON amplicon name --dada2directory DADA2DIRECTORY DADA2 directory with inputs --workingdirectory WORKINGDIRECTORY working directory --minasvreadcount MINASVREADCOUNT asv total read count threshold --minsamplereadcount MINSAMPLEREADCOUNT sample total read count threshold --maxtargetseq MAXTARGETSEQ blastn maxtargetseq --artefactcutoff ARTEFACTCUTOFF artefact filter (coverage & identity) --mincoverage MINCOVERAGE percent coverage filter --minidentity MINIDENTITY percent identity filter --lwrcutoff LWRCUTOFF Like Weight Ratio cutoff --maxhaplotypespersample MAXHAPLOTYPESPERSAMPLE maximum number of ASVs for batch-level --minabundanceassignment MINABUNDANCEASSIGNMENT minimum ASV read count abundance --tempdir TEMPDIR temporary directory --referencetree REFERENCETREE reference tree --referencemsa REFERENCEMSA reference msa --referencedatabase REFERENCEDATABASE reference BLAST database --blastonly only run blastn --runblast run blast --runmsa run msa --runtree run tree ```

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