All pages prior to Microbiome Helper 2 - LangilleLab/microbiome_helper GitHub Wiki

To make it easy to see all previous versions of pages, we have listed them here:

• Home - last updated Dec 4, 2024
• 16S Bacteria and Archaea Standard Operating Procedure - last updated Jan 30, 2018
• 16S tutorial (chemerin) - last updated Apr 4, 2020
• 16S tutorial (long running time) - last updated May 16, 2016
• 16S tutorial answers - last updated Apr 4, 2020
• 16S tutorial for CCBC - last updated Sep 26, 2016
• 18S Eukarya Standard Operating Procedure - last updated Mar 26, 2018
• 2017 Summer School - last updated Jun 21, 2017
• Additional QIIME analysis - last updated Sep 26, 2016
• Alpha and beta diversity - last updated Apr 13, 2016
• Alternative Processing of Reads with PEAR - last updated Dec 14, 2021
• Amplicon detailed resources - last updated Jan 30, 2018
• Amplicon SOP v2 (qiime2 2018.6) - last updated Feb 6, 2020
• Amplicon SOP v2 (qiime2 2018.8) - last updated Jul 30, 2019
• Amplicon SOP v2 (qiime2 2019.10) - last updated Feb 6, 2020
• Amplicon SOP v2 (qiime2 2019.7) - last updated Aug 11, 2021
• Amplicon SOP v2 (qiime2 2020.2) - last updated May 6, 2020
• Amplicon SOP v2 (qiime2 2020.8) - last updated Jul 25, 2023
• Amplicon SOP v2 (qiime2 2022.11) - last updated Oct 21, 2024
• Amplicon SOP v2 (qiime2‐2024.5) - last updated Dec 2, 2024
• Answers to questions (2023 ICG) - last updated May 25, 2023
• BIOC4010 16S Tutorial - last updated Apr 10, 2024
• Brief description of scripts - last updated Jul 10, 2018
• CBW 2016 Metagenomic Taxonomic Tutorial - last updated Jun 22, 2016
• CBW 2016 Metagenomics Functional Tutorial - last updated Jul 23, 2016
• CBW 2016 Metagenomics Tutorial Answers - last updated Jun 22, 2016
• CBW 2016 PICRUSt tutorial - last updated Jan 5, 2018
• CBW 2018 Metagenomic Taxonomic and Functional Composition Tutorial - last updated Jun 6, 2018
• CBW 2018 Metagenomic Taxonomic and Functional Composition Tutorial Answers - last updated Jun 2, 2018
• CBW 2018 PICRUSt2 Tutorial - last updated Oct 19, 2018
• CBW 2018 PICRUSt2 Tutorial Answers - last updated Jun 1, 2018
• CBW 2021 Metagenomic Taxonomic and Functional Composition Tutorial - last updated Sep 2, 2021
• CBW 2021 Metagenomic Taxonomic and Functional Composition Tutorial Answers - last updated Aug 31, 2021
• CBW 2021 PICRUSt2 Tutorial - last updated Aug 27, 2021
• CBW 2021 PICRUSt2 Tutorial Answers - last updated Aug 27, 2021
• CBW 2024 Advanced Module 1: Introduction to metagenomics and read‐based profiling - last updated May 28, 2024
• CBW 2024 Advanced Module 2: Metagenomic Assembly and Binning - last updated May 29, 2024
• CBW 2024 Advanced Module 3: Metagenomic functional annotation - last updated May 24, 2024
• CBW 2024 Advanced Module 4: Advanced microbiome statistics - last updated May 30, 2024
• CBW 2024 Beginner Module 1: Introduction to sequencing data analysis - last updated May 21, 2024
• CBW 2024 Beginner Module 2: Marker gene profiling - last updated Apr 30, 2024
• CBW 2024 Beginner Module 3: Microbiome statistics and visualizations - last updated Apr 30, 2024
• CBW 2024 Beginner Module 4: Functional prediction and additional analyses - last updated May 26, 2024
• CBW 2024 workshops (overview) - last updated Jul 10, 2024
• CBW IMPACTT 2023 answers - last updated Jul 4, 2023
• CBW IMPACTT 2023 Microbiome analysis using QIIME2 with 16S data - last updated Jul 4, 2024
• CBW IMPACTT Metagenome sequence data analysis with Kraken2 and Phyloseq - last updated Jul 4, 2023
• CBW IMPACTT Metagenome sequence data analysis with MMSeqs2 and JarrVis - last updated Jul 4, 2023
• CBW IMPACTT workshop tutorials 2023 - last updated Jul 6, 2023
• CBW workshop 2024 advanced - last updated May 21, 2024
• CBW workshop 2024 beginner - last updated May 21, 2024
• CBW‐ICG Advanced Microbiome Analysis Module1 - last updated Jul 11, 2024
• CBW‐ICG Advanced Microbiome Analysis Module2 - last updated Jul 11, 2024
• CBW‐ICG Advanced Microbiome Analysis Module3 - last updated Jul 12, 2024
• CBW‐ICG Advanced Microbiome Analysis Module4 - last updated Jul 12, 2024
• CBW‐ICG Beginner Microbiome Analysis Module1 - last updated Jul 7, 2024
• CBW‐ICG Beginner Microbiome Analysis Module2 - last updated Jul 7, 2024
• CBW‐ICG Beginner Microbiome Analysis Module3 - last updated Jul 5, 2024
• CBW‐ICG Beginner Microbiome Analysis Module4 - last updated Jul 7, 2024
• CBW‐IMPACTT metagenomic taxonomic and functional annotation - last updated Jul 6, 2023
• CCBC Workshop 2016 - last updated Sep 29, 2017
• Creating primer specific QIIME 2 taxonomic classifiers - last updated Nov 2, 2020
• Creating QIIME 2 Taxonomic Classifiers - last updated Jul 4, 2024
• DADA2 16S Chemerin Tutorial - last updated Jul 10, 2018
• Download_From_SRA - last updated Oct 17, 2017
• Functional profiling - last updated Oct 4, 2017
• ICG workshop 2023 - last updated May 21, 2023
• IMPACTT workshop tutorials 2022 - last updated May 19, 2023
• Introduction to Unix - last updated May 26, 2023
• Introductory Linux Quiz - last updated Nov 14, 2016
• IonTorrent Amplicon SOP v1 (qiime2) - last updated May 6, 2020
• ITS2 Fungi Standard Operating Procedure - last updated Jan 30, 2018
• Metagenome sequence data analysis with Kraken2 and Phyloseq - last updated May 25, 2023
• Metagenomic standard operating procedure - last updated Jan 30, 2018
• Metagenomics (answers; IMPACTT 2022) - last updated May 30, 2022
• Metagenomics (functional annotation; IMPACTT 2022) - last updated Jun 24, 2022
• Metagenomics (IMPACTT December 2022) - last updated Dec 13, 2022
• Metagenomics (IMPACTT December 2022) Answers - last updated Dec 7, 2022
• Metagenomics (IMPACTT December 2022) Assembly - last updated Dec 6, 2022
• Metagenomics (IMPACTT December 2022) Pre workshop - last updated Nov 28, 2022
• Metagenomics (IMPACTT December 2022) Taxonomic annotation - last updated Dec 7, 2022
• Metagenomics (taxonomic annotation; IMPACTT 2022) - last updated Jun 23, 2022
• Metagenomics Resources - last updated Jan 30, 2018
• Metagenomics Sequencing Pre processing - last updated Mar 25, 2019
• Metagenomics standard operating procedure v2 - last updated Oct 4, 2020
• Metagenomics Standard Operating Procedure v3 - last updated Jul 17, 2024
• Metagenomics Tutorial (Humann1) - last updated Jun 11, 2021
• Metagenomics Tutorial (HUMAnN2) - last updated Jun 7, 2023
• Metagenomics Tutorial (Long Running) - last updated Apr 10, 2017
• Metagenomics Tutorial (Long Running) Answers - last updated Apr 10, 2017
• Metagenomics Tutorial (Older) - last updated Apr 10, 2017
• Metagenomics Tutorial (Older) answers - last updated Apr 10, 2017
• Metagenomics Tutorial Answers - last updated Oct 5, 2017
• Metagenomics Tutorial Answers (HUMAnN1) - last updated Oct 5, 2017
• Microbial diversity metrics and data visualization with QIIME2 - last updated May 25, 2023
• Microbiome Amplicon Sequencing Workflow - last updated May 7, 2020
• Microbiome analysis using QIIME2 with 16S data - last updated Apr 18, 2024
• Microbiome for beginners - last updated Sep 11, 2023
• Microbiome Helper Virtual Box - last updated Jun 7, 2021
• MicrobiomeHelper Virtual Box - last updated Apr 3, 2017
• mSystems paper data - last updated Feb 22, 2017
• Old SOPs - last updated Dec 2, 2024
• Other Tutorials - last updated Dec 2, 2024
• OTU picking - last updated Feb 17, 2016
• PacBio CCS Amplicon SOP v1 (qiime2) - last updated Jul 27, 2022
• PacBio CCS Amplicon SOP v2 (qiime2 2022.2) - last updated Oct 21, 2024
• Past SOP databases - last updated Apr 3, 2020
• PICRUSt tutorial - last updated Jun 20, 2017
• PICRUSt Tutorial Answers - last updated Aug 5, 2016
• PICRUSt Tutorial with de novo Variants - last updated Sep 6, 2018
• PICRUSt workflow - last updated Nov 3, 2017
• Predict phenotypes - last updated Nov 30, 2016
• QIIME 2 de novo tree creation - last updated Jan 15, 2020
• QIIME2 DADA2 Quick Reference - last updated Jun 29, 2020
• Quick Introduction to GNU Parallel - last updated Mar 30, 2023
• Random Forest Feature Selection Caution - last updated Mar 10, 2017
• Random Forest in R with Large Sample Sizes - last updated Oct 24, 2019
• Random Forest Tutorial - last updated Mar 26, 2020
• Remove chimeric reads - last updated Jun 21, 2017
• Remove low quality reads - last updated Oct 27, 2016
• Requirements - last updated Aug 19, 2021
• Sequence error correction - last updated Dec 2, 2016
• Sequence QC - last updated Feb 17, 2016
• Setting up an AWS instance with the CBW AMI - last updated Jun 7, 2024
• Software References - last updated Sep 5, 2017
• STAMP preparation - last updated Jan 30, 2021
• STAMPS 2016 PICRUSt Tutorial - last updated Aug 5, 2016
• Stitch reads - last updated May 11, 2016
• Subsampling Metagenomic FASTQs - last updated Oct 5, 2017
• Taxonomic composition - last updated Oct 5, 2017
• Viromics Pipeline - last updated Mar 5, 2019