Royal Botanic Gardens Victoria

AAToL

Scripts and pipelines for Australian Angiosperm Tree of Life Paper

DNA_entropy_scripts

Python scripts for calculating and filtering DNA entropy

gap-download

Downloads files from the GAP data portal https://data.bioplatforms.com/organization/about/bpa-plants

GAP_hybpiper_helpers

Helper / wrapper scripts for running Hybpiper2 on NCI Gadi.

genomes_update

Search NCBI for latest genome and sequence data for a specified taxon

HybPiper-RBGV

Nextflow/Singularity pipeline for running modified scripts from HybPiper (https://github.com/mossmatters/HybPiper)

NanoFungiBarcode

PAFTOL-taxonomy-classifier

#Scripts to create Kraken2 database of PAFTOL V2.0 Angio353 genes. An excellent database for taxonomic identification of plants. #https://treeoflife.kew.org/ #https://github.com/DerrickWood/kraken2/wiki #Prior to using this script, download and install kraken2 and make sure it is working and in your PATH. #Make sure the location of the python scripts used below are also in your PATH #Download PAFTOL V2.0 Angio353 genes from Kew #After building the DB, the scripts kraken2paired.py and top_taxa.py can be used to identify taxonomy of unknown samples. #e.g. #kraken2paired.py "reads/*.fastq" kraken_results/ 0 24 kraken2_paftol2/ #top_taxa.py "kraken_results/*" kraken.out

species2taxid.py

Fetches the NCBI TaxID and full taxonomy from list of species names.

VicMicrobiome

Soil meta-barcoding across the state of Victoria, Australia

Royal-Botanic-Gardens-Victoria/VicMicrobiome

Soil meta-barcoding across the state of Victoria, Australia

Royal-Botanic-Gardens-Victoria/PAFTOL-taxonomy-classifier

#Scripts to create Kraken2 database of PAFTOL V2.0 Angio353 genes. An excellent database for taxonomic identification of plants. #https://treeoflife.kew.org/ #https://github.com/DerrickWood/kraken2/wiki #Prior to using this script, download and install kraken2 and make sure it is working and in your PATH. #Make sure the location of the python scripts used below are also in your PATH #Download PAFTOL V2.0 Angio353 genes from Kew #After building the DB, the scripts kraken2paired.py and top_taxa.py can be used to identify taxonomy of unknown samples. #e.g. #kraken2paired.py "reads/*.fastq" kraken_results/ 0 24 kraken2_paftol2/ #top_taxa.py "kraken_results/*" kraken.out

Royal-Botanic-Gardens-Victoria/AAToL

Scripts and pipelines for Australian Angiosperm Tree of Life Paper

Royal-Botanic-Gardens-Victoria/DNA_entropy_scripts

Python scripts for calculating and filtering DNA entropy

Royal-Botanic-Gardens-Victoria/gap-download

Downloads files from the GAP data portal https://data.bioplatforms.com/organization/about/bpa-plants

Royal-Botanic-Gardens-Victoria/GAP_hybpiper_helpers

Helper / wrapper scripts for running Hybpiper2 on NCI Gadi.

Royal-Botanic-Gardens-Victoria/genomes_update

Search NCBI for latest genome and sequence data for a specified taxon

Royal-Botanic-Gardens-Victoria/HybPiper-RBGV

Nextflow/Singularity pipeline for running modified scripts from HybPiper (https://github.com/mossmatters/HybPiper)

Royal-Botanic-Gardens-Victoria/NanoFungiBarcode

Royal-Botanic-Gardens-Victoria/species2taxid.py

Fetches the NCBI TaxID and full taxonomy from list of species names.

Royal-Botanic-Gardens-Victoria/taxonkit

A Practical and Efficient NCBI Taxonomy Toolkit

Royal-Botanic-Gardens-Victoria/turbo_scripts

Parallelises common commands