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Training and Workshops
2023
2024
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Introduction to R
2024 - Semester One: Hands-on variant calling and metagenomics analyses using QUT's HPC and Nextflow
Session 1 - Intro to HPC
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What is the HPC?
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Connecting to the HPC
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Transferring Data to and from the HPC
Using the Shell
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Software on the HPC
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Submitting PBS Jobs
Session 2 - Variant calling analysis
Session 3 - Variant analysis using Nanopore data
Session 4: Metagenomics (amplicon sequencing analysis)
Session 5: Analysis of amplicon sequencing results in R
2024 - Semester Two: Hands on training workshops - HPC and Gene Expression (RNAseq and small RNAseq) analyses
Start using the HPC
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eResearch - single cell RNA-Seq analysis (10x Genomics)
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eResearch - writing Nextflow workflows, beginner's guide
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2024 eResearch - Session 6 - Hands-on smRNAseq training
Data Download
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NextFlow quick start
nf-core/rnaseq - Gene Expression Analysis
nf-core/smrnaseq - Small RNA seq Analysis
nf-core/sarek - variant calling pipeline
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nf-core/bactmap: A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
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nf-epi2me-labs/wf-transcriptomes
nf-eresearch/ONTprocessing - NextFlow pipeline for Oxford Nanopore de novo assembly and ref guided consensus
nf-eresearch/ConsGenome: Nextflow based Genome Assembly, Variant Calling and building a Consensus Genome workflow
nf-eresearch/VirReport - Diagnosis of plant viruses and viroids using small RNA-seq data
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nf-core/hic: Analysis of Chromosome Conformation Capture data (Hi-C)
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nf-core/ampliseq 16S amplicon analysis pipeline (NextFlow Ampliseq)
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nf-core/scrnaseq: A single-cell RNAseq pipeline for 10X genomics data
DESeq2 - Differential expression analysis
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PacBio SMRT full length 16S analysis
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PacBio SMRT command line Iso-seq analysis
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ONT de novo genome assembly
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ONT Oxford Nanopore fast5 processing
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Variant filtering - screening homozygous recessive mutations
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Anacapa - eDNA analysis toolkit
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Automatic Assembly For The Fungi (AAFTF) pipeline
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Extracting unmapped sequences
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primalscheme - designing primer panels for multiplex PCR
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Uploading sequence data to SRA
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Copy of Copy of Hands-on smRNAseq training
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Merging oligonucleotide sequences (local, HPC)
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Bisulfite conversion WGBS
Equus caballus Project
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Snakemake at QUT
ChIP-Seq
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EBV genome integration data analysis
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Common Nextflow errors
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How to perform KEGG and GO enrichment analysis of non-model species (using R)
Legacy user guides
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Nanostring - Nanostring DSP protein assay data QC, exploration, normalisation and analysis.
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draw.io Diagrams
ER-User Guides
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2024 - Semester One: Hands-on variant calling and metagenomics analyses using QUT's HPC and Nextflow
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Session 1 - Intro to HPC
Summarize
Session 1 - Intro to HPC
Craig Windell
Owned by
Craig Windell
Last updated:
Apr 30, 2024
1 min read
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Accessing and using QUT's HPC
Open
hbctraining/Intro-to-shell-flipped (github.com)
Accessing and using the HPC information is over the following pages:
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