Page Index - LangilleLab/microbiome_helper GitHub Wiki

145 page(s) in this GitHub Wiki:

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