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10xgenomics

Pipeline for the 10x Genomics read processing

aigd

This is a hybrid pipeline to unvocer the genetic make up of avian species that is responsible for innate immune responses to Influenza A virus

black_swan_genome_assembly

This repository contains the scripts used for black swan (Cygnus atratus) genome assembly using PacBio long reads sequence data. The black swan gneome was constructed as a part of a project investigating genesis and pathogenesis of highly pathogenic avian influenza in Australian black swans. The study was conducted at the University of Queensland, St. Lucia, Queensland, 4027.

caln50

Compute N50/NG50 and auN/auNG

chelonia_mydas_project_hannon_et_al

This project investigates the transcriptional profile of natural green turtles (Chelonia mydas) in Australia

dorado

Oxford Nanopore's Basecaller

falcon-manually

For users who can't get PacBio's https://github.com/PacificBiosciences/FALCON-integrate assembler running on their cluster

flye

De novo assembler for single molecule sequencing reads using repeat graphs

gene_family_evolution_in_swans

The gene family evolution in swans with OrthoFinder/CAFE5

hulme_et_al

Scripts for the manuscript submission

ibisomics

Assembly and annotation of Australian Native Ibises

kofamscan

This repository contains information on how to run the kofamscan for a given set of proteins for KEGG based annotation

kraken2

The second version of the Kraken taxonomic sequence classification system

longest_isoforms

marcus_z_w_tong_et_al

R scripts for Tong_et_al_paper

mhc_complex_annotation_of_swans

This pipeline describes on how to annotate MHC class I and II genes in both mute swan and black swan

necat

Nanopore data assembler

nextstrain_sri_lanka_ncov

Evolutionary genomics of SARS-COV2 Sri Lankan Strains as a Nextstrain Build

palu_calu_transcriptional_profiling

This repository contains the codes and scripts used for comparative transcriptomic analysis of PaLu and CaLu SARSCoV2 in vitro modelling

ratite-genomics

Scripts and other material for the assembly and analysis of ratite genomes.

rna-seq-analysis-of-endothelial_cells

This repositroy contains scripts to run RNA-seq differential gene expression analysis for avian endothelial cell infection

running_dorado

seurat

R toolkit for single cell genomics

slurm_cook

Simple commands

stlfr2supernova_pipeline

A pipeline to de novo assemble the stLFR reads using Supernova Assembler

sumopac

A piepline for metatranscriptomics using ONT MinIon direct RNA seqeucing

swan_genome_annotation

maker3 annotation for swan genomes using the transcriptomic evidence, homology evidence and de novo prediction

swan_genomics_and_transcriptomics

synteny-analysis-with-progressivecactus-and-mummer

This pipeline describes the method of multiple avian genome analysis and synteny analysis

vgp-assembly-mute-swan

VGP repository for the genome assembly working group