Pipeline to run qiime2 with snakemake
☆18Apr 17, 2020Updated 5 years ago
Alternatives and similar repositories for tagseq-qiime2-snakemake
Users that are interested in tagseq-qiime2-snakemake are comparing it to the libraries listed below
Sorting:
- Amplicon sequence processing workflow using QIIME 2 and Snakemake☆44Dec 22, 2025Updated 2 months ago
- Automated pipeline for amplicon sequence analysis☆11Nov 25, 2025Updated 3 months ago
- Analysing Metagenomic Species (MGS)☆42Nov 12, 2020Updated 5 years ago
- Code for de novo discovery of viral families in virome data☆16Jun 20, 2024Updated last year
- Strain-level abundances estimation in metagenomic samples using variation graphs☆24Jan 29, 2023Updated 3 years ago
- A taxonomic classifier for shotgun metagenomics reads☆11Apr 4, 2025Updated 11 months ago
- Standard tools and protocols for MiSeq amplicon sequencing of 16S rRNA genes☆10Nov 14, 2022Updated 3 years ago
- MetaflowX: A Scalable and Resource-Efficient Workflow for Multi-Strategy Metagenomic Analysis☆30Feb 6, 2026Updated last month
- Some useful python scripts for biologists☆32Nov 19, 2024Updated last year
- Metalign: efficient alignment-based metagenomic profiling via containment min hash☆33Sep 12, 2023Updated 2 years ago
- A pipeline based on EMU, a taxonomic profiler optimized for long 16S rRNA reads.☆19Feb 27, 2026Updated last week
- INC-Seq: Accurate single molecule reads using nanopore sequencing☆16Sep 11, 2020Updated 5 years ago
- MetaProFi is a bloom filter based tool for storing and querying sequence data for accurate identification of functionally relevant geneti…☆12Apr 14, 2022Updated 3 years ago
- Quantitative Microbiome Profiling☆15Mar 13, 2021Updated 4 years ago
- A repo with just adapter sequences☆15Jul 7, 2025Updated 8 months ago
- ☆15Oct 7, 2025Updated 5 months ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆34Dec 4, 2025Updated 3 months ago
- Stitch together Nanopore tiled amplicon data without polishing a reference☆17Jan 29, 2024Updated 2 years ago
- Bioinformatic Tools for analyzing targeted amplicon sequencing developed by Nicholas Hathaway of Bailey Lab☆17Updated this week
- An R Package for Integrated Analysis and Visualization of Microbiome Data☆18Feb 19, 2026Updated 2 weeks ago
- strain-level analysis tools☆39Oct 21, 2024Updated last year
- Amplicon sequencing analysis workflow using DADA2 and QIIME2☆236Feb 23, 2026Updated 2 weeks ago
- MegaPath-Nano: Accurate Compositional Analysis and Drug-level Antimicrobial Resistance Detection Software for Oxford Nanopore Long-read M…☆13Jul 2, 2022Updated 3 years ago
- genome sized sequences clustering☆17Dec 29, 2020Updated 5 years ago
- The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…☆19May 3, 2024Updated last year
- Long read metagenomics practical at EBAME18☆18Oct 3, 2018Updated 7 years ago
- ☆19Dec 4, 2025Updated 3 months ago
- Qiime2 snakemake pipeline☆20Dec 21, 2023Updated 2 years ago
- Spaghetti: in situ analysis of 16S rRNA amplicons obtained by nanopore sequencing☆20Jul 26, 2024Updated last year
- Generate de novo taxonomy of full length 16S rRNA sequences directly from environmental samples☆20Nov 23, 2024Updated last year
- StrainEst - abundance estimation of strains☆20Jan 17, 2020Updated 6 years ago
- A Python package for microbiome sequencing analysis with QIIME 2☆47Jan 28, 2024Updated 2 years ago
- Course material for the metagenomics course☆47Mar 2, 2022Updated 4 years ago
- bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validate…☆129Oct 20, 2025Updated 4 months ago
- Strain Prediction and Analysis with Representative SEquence☆19Dec 8, 2024Updated last year
- TADA - Targeted Amplicon Diversity Analysis - a DADA2-focused Nextflow workflow for any targeted amplicon region☆22Dec 11, 2025Updated 2 months ago
- Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake☆50Mar 6, 2024Updated 2 years ago
- An integrated pipeline for estimating strain-level genomic variation from metagenomic data☆132Oct 6, 2023Updated 2 years ago
- MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achiev…☆24Jun 9, 2021Updated 4 years ago