Julian Zaugg's repositories
aviary
A snakemake pipeline for binning metagenomic assemblies
B04Sm5_genome_completion
Completing and closing the genome of Streptococcus mutans strain B04Sm5 using composite long and short-read sequencing.
Bayesian_Network_Python
Create and parameterise bayesian networks
bioinformatics_scripts
Random collection of scripts used for bioinformatics analyses. May or may not function. Most written by me.
ccfind
ccfind - circular complete genome finder with clues of terminal redundancy
Example_qiime2
Example (somewhat hacky) script for running qiime2 on ACE's servers for amplicon data
Fix_NCBI_MAG_submission
Fix automated errors during the submission of MAGs to NCBI due to adaptors by removing problematic regions
katuali
Analysis pipelines from Oxford Nanopore Technologies' Research Division
MET
GIH MET pipeline
OM_respiratory_tract_16S_2021
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"
pairwiseAdonis
Pairwise multilevel comparison using adonis
PDProcessing
Package to handle processing of results file from PairDistances java package
PIGC
The construction of reference gene catalog and metagenome-assembled genomes of pig gut microbiome.
Skin_microbiome_SCC_OTR_rRNA_2021
Analysis scripts for "Changes in the skin microbiome associated with squamous cell carcinoma in transplant recipients"
TVBOT
Beautify the phylogenetic tree using one Excel sheet only
variable_rate_testing
Compare ancestral reconstruction tools
veba
A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
viral_annotate
Simple snakemake pipeline to annotate viral sequences.