Page Index - LangilleLab/microbiome_helper GitHub Wiki

323 page(s) in this GitHub Wiki:

• Home
• 16S Bacteria and Archaea Standard Operating Procedure
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• 16S tutorial (chemerin)
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• 16S tutorial (long running time)
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• 16S tutorial answers
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• 16S tutorial for CCBC
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• 18S Eukarya Standard Operating Procedure
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• 2017 Summer School
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• Additional QIIME analysis
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• All pages prior to Microbiome Helper 2
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• Alpha and beta diversity
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• Alternative Processing of Reads with PEAR
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• Amplicon Detailed Resources
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• Amplicon SOP v2 (qiime2 2018.6)
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• Amplicon SOP v2 (qiime2 2018.8)
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• Amplicon SOP v2 (qiime2 2019.10)
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• Amplicon SOP v2 (qiime2 2019.7)
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• Amplicon SOP v2 (qiime2 2020.2)
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• Amplicon SOP v2 (qiime2 2020.8)
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• Amplicon SOP v2 (qiime2 2022.11)
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• Amplicon SOP v2 (qiime2‐2024.5)
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• Answers to questions
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• Antofagasta 2025 workshop
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• BIOC4010 16S Tutorial
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• Brief description of scripts
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• CBW 2016 Metagenomic Taxonomic Tutorial
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• CBW 2016 Metagenomics Functional Tutorial
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• CBW 2016 Metagenomics Tutorial Answers
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• CBW 2016 PICRUSt tutorial
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• CBW 2018 Metagenomic Taxonomic and Functional Composition Tutorial
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• CBW 2018 Metagenomic Taxonomic and Functional Composition Tutorial Answers
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• CBW 2018 PICRUSt2 Tutorial
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• CBW 2018 PICRUSt2 Tutorial Answers
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• CBW 2021 Metagenomic Taxonomic and Functional Composition Tutorial
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• CBW 2021 Metagenomic Taxonomic and Functional Composition Tutorial Answers
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• CBW 2021 PICRUSt2 Tutorial
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• CBW 2021 PICRUSt2 Tutorial Answers
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• CBW 2024 Advanced Module 1: Introduction to metagenomics and read‐based profiling
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• CBW 2024 Advanced Module 2: Metagenomic Assembly and Binning
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• CBW 2024 Advanced Module 3: Metagenomic functional annotation
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• CBW 2024 Advanced Module 4: Advanced microbiome statistics
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• CBW 2024 Beginner Module 1: Introduction to sequencing data analysis
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• CBW 2024 Beginner Module 2: Marker gene profiling
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• CBW 2024 Beginner Module 3: Microbiome statistics and visualizations
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• CBW 2024 Beginner Module 4: Functional prediction and additional analyses
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• CBW 2024 workshops
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• CBW 2025 workshops
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• CBW IMPACTT 2023 answers
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• CBW IMPACTT 2023 Microbiome analysis using QIIME2 with 16S data
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• CBW IMPACTT Metagenome sequence data analysis with Kraken2 and Phyloseq
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• CBW IMPACTT Metagenome sequence data analysis with MMSeqs2 and JarrVis
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• CBW IMPACTT workshop tutorials 2023
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• CBW workshop 2024 advanced
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• CBW workshop 2024 beginner
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• CBW‐2025‐AMB‐Module1
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• CBW‐2025‐BMB‐Module1
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• CBW‐2025‐BMB‐Module2
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• CBW‐2025‐BMB‐Module3
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• CBW‐2025‐BMB‐Module4
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• CBW‐ICG‐AMB‐Module1
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• CBW‐ICG‐AMB‐Module2
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• CBW‐ICG‐AMB‐Module3
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• CBW‐ICG‐AMB‐Module4
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• CBW‐ICG‐BMB‐Module1
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• CBW‐ICG‐BMB‐Module2
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• CBW‐ICG‐BMB‐Module3
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• CBW‐ICG‐BMB‐Module4
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• CBW‐IMPACTT metagenomic taxonomic and functional annotation
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• CCBC Workshop 2016
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• Creating primer specific QIIME 2 taxonomic classifiers
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• Creating QIIME 2 Taxonomic Classifiers
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• DADA2 16S Chemerin Tutorial
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• Download_From_SRA
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• Functional profiling
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• Home ‐ Microbiome Helper 2
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• ICG workshop 2023
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• IMPACTT workshop tutorials 2022
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• Introduction to Unix
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• Introductory Linux Quiz
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• IonTorrent Amplicon SOP v1 (qiime2)
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• ITS2 Fungi Standard Operating Procedure
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• Metagenome sequence data analysis with Kraken2 and Phyloseq
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• Metagenomic standard operating procedure
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• Metagenomics (answers; IMPACTT 2022)
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• Metagenomics (functional annotation; IMPACTT 2022)
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• Metagenomics (IMPACTT December 2022)
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• Metagenomics (IMPACTT December 2022) Answers
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• Metagenomics (IMPACTT December 2022) Assembly
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• Metagenomics (IMPACTT December 2022) Pre workshop
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• Metagenomics (IMPACTT December 2022) Taxonomic annotation
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• Metagenomics (taxonomic annotation; IMPACTT 2022)
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• Metagenomics Resources
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• Metagenomics Sequencing Pre processing
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• Metagenomics standard operating procedure v2
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• Metagenomics Standard Operating Procedure v3
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• Metagenomics Tutorial (Humann1)
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• Metagenomics Tutorial (HUMAnN2)
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• Metagenomics Tutorial (Long Running)
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• Metagenomics Tutorial (Long Running) Answers
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• Metagenomics Tutorial (Older)
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• Metagenomics Tutorial (Older) answers
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• Metagenomics Tutorial Answers
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• Metagenomics Tutorial Answers (HUMAnN1)
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• Microbial diversity metrics and data visualization with QIIME2
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• Microbiome Amplicon Sequencing Workflow
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• Microbiome analysis using QIIME2 with 16S data
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• Microbiome for beginners
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• Microbiome Helper 2 Amplicon basic statistics and visualisation
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• Microbiome Helper 2 Analysis workflow in R
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• Microbiome Helper 2 Annotation of reads contigs with CARD RGI
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• Microbiome Helper 2 Annotation of reads with Kraken2 (and taxonomic profiling with Bracken)
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• Microbiome Helper 2 Annotation of reads with MMSeqs2
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• Microbiome Helper 2 Annotation with MetaPhlAn
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• Microbiome Helper 2 Brief introduction to the command line
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• Microbiome Helper 2 Checking coverage of obtained annotations
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• Microbiome Helper 2 Functional annotation of metagenomic reads with HMMs
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• Microbiome Helper 2 Functional profiling with HUMAnN
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• Microbiome Helper 2 Getting a phylogenetic taxonomic tree (metagenome)
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• Microbiome Helper 2 Linking functions with taxonomy
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• Microbiome Helper 2 MAG assembly, binning, and curation with Anvi'o
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• Microbiome Helper 2 Making Kraken2 and Bracken databases
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• Microbiome Helper 2 Marker gene workflow
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• Microbiome Helper 2 Metagenomics initial Steps
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• Microbiome Helper 2 PICRUSt2
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• Microbiome Helper 2 Setting up environments for analysis
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• Microbiome Helper 2 Taxonomic profiling with Sylph
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• Microbiome Helper 2 Tutorial data
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• Microbiome Helper 2 Useful code
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• Microbiome Helper Virtual Box
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• MicrobiomeHelper Virtual Box
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• mSystems paper data
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• Old SOPs
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• Other Tutorials
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• OTU picking
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• PacBio CCS Amplicon SOP v1 (qiime2)
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• PacBio CCS Amplicon SOP v2 (qiime2 2022.2)
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• PacBio CCS Amplicon SOP v2 (qiime2 2024.10)
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• Past SOP databases
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• PICRUSt tutorial
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• PICRUSt Tutorial Answers
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• PICRUSt Tutorial with de novo Variants
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• PICRUSt workflow
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• Predict phenotypes
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• QIIME 2 de novo tree creation
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• QIIME2 DADA2 Quick Reference
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• Quick Introduction to GNU Parallel
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• Random Forest Feature Selection Caution
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• Random Forest in R with Large Sample Sizes
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• Random Forest Tutorial
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• Remove chimeric reads
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• Remove low quality reads
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• Requirements
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• Sequence error correction
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• Sequence QC
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• Setting up an AWS instance with the CBW AMI
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• Software References
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• STAMP preparation
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• STAMPS 2016 PICRUSt Tutorial
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• Stitch reads
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• Subsampling Metagenomic FASTQs
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• Taxonomic composition
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• Viromics Pipeline
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