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  • Australian Centre for Ecogenomics

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@Ecogenomics @bodenlab

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  • MAP Public

    Microbiome analysis package (MAP)

    R Other Updated Aug 8, 2024

  • MET Public

    Forked from vmurigneu/MET

    GIH MET pipeline

    Nextflow Updated Apr 11, 2024

  • Fix_NCBI_MAG_submission Public

    Forked from katherinedougan/Fix_NCBI_MAG_submission

    Fix automated errors during the submission of MAGs to NCBI due to adaptors by removing problematic regions

    Python Updated Mar 6, 2024

  • veba Public

    Forked from jolespin/veba

    A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

    Python GNU Affero General Public License v3.0 Updated Oct 17, 2023

  • julianzaugg.github.io Public

    HTML Updated Mar 9, 2023

  • TVBOT Public

    Forked from 1996xjm/TVBOT

    Beautify the phylogenetic tree using one Excel sheet only

    HTML Updated Jan 31, 2023

  • CFphage_pipe Public

    Python Updated Jun 29, 2022

  • viral_annotate Public

    Simple snakemake pipeline to annotate viral sequences.

    Python Updated Jun 15, 2022

  • aviary Public

    Forked from rhysnewell/aviary

    A snakemake pipeline for binning metagenomic assemblies

    Python BSD 3-Clause "New" or "Revised" License Updated May 13, 2022

  • bioinformatics_scripts Public

    Random collection of scripts used for bioinformatics analyses. May or may not function. Most written by me.

    Python Updated Apr 6, 2022

  • Example_qiime2 Public

    Example (somewhat hacky) script for running qiime2 on ACE's servers for amplicon data

    Shell Updated Nov 16, 2021

  • Skin_microbiome_SCC_OTR_rRNA_2021 Public

    Analysis scripts for "Changes in the skin microbiome associated with squamous cell carcinoma in transplant recipients"

    R Updated Aug 2, 2021

  • OM_respiratory_tract_16S_2021 Public

    Analysis scripts and data for "The upper respiratory tract microbiome of Australian Aboriginal and Torres Strait Islander children in ear and nose health and disease; a prospective cohort study"

    R Updated Mar 25, 2021

  • otitis_project Public

    R Updated Mar 24, 2021

  • skin_microbiome_16S Public

    R Updated Mar 18, 2021

  • PIGC Public

    Forked from zhouyunyan/PIGC

    The construction of reference gene catalog and metagenome-assembled genomes of pig gut microbiome.

    R Updated Jan 4, 2021

  • B04Sm5_genome_completion Public

    Forked from jaybake5/B04Sm5_genome_completion

    Completing and closing the genome of Streptococcus mutans strain B04Sm5 using composite long and short-read sequencing.

    Shell Updated Oct 22, 2020

  • ccfind Public

    Forked from yosuken/ccfind

    ccfind - circular complete genome finder with clues of terminal redundancy

    Ruby MIT License Updated Jul 9, 2020

  • Compare_Compounds Public

    Python Updated Jun 28, 2020

  • PhagePipe Public

    Python Updated Jun 27, 2020

  • pairwiseAdonis Public

    Forked from pmartinezarbizu/pairwiseAdonis

    Pairwise multilevel comparison using adonis

    R GNU General Public License v3.0 Updated Jun 18, 2020

  • mine_waste Public

    R Updated May 12, 2020

  • katuali Public

    Forked from nanoporetech/katuali

    Analysis pipelines from Oxford Nanopore Technologies' Research Division

    Python Other Updated Mar 10, 2020

  • Metagenomics-Index-Correction Public

    Forked from rrwick/Metagenomics-Index-Correction
    Python GNU General Public License v3.0 Updated Aug 7, 2019

  • get_neighbours Public

    Python Updated Aug 10, 2018

  • md_scripts Public

    Python Updated Jan 11, 2018

  • Various-Scripts Public

    Python Updated Dec 21, 2017

  • Bayesian_Network_Python Public

    Create and parameterise bayesian networks

    Python Updated Nov 27, 2017

  • PDProcessing Public

    Package to handle processing of results file from PairDistances java package

    Python Updated Aug 17, 2017

  • variable_rate_testing Public

    Compare ancestral reconstruction tools

    Python Updated Aug 8, 2017