General procedure for making QIIME 2 compatible SILVA reference files
☆20Oct 3, 2024Updated last year
Alternatives and similar repositories for make_SILVA_db
Users that are interested in make_SILVA_db are comparing it to the libraries listed below
Sorting:
- Reproducible Analyses accompanying DADA2 + PacBio Manuscript☆34Oct 26, 2020Updated 5 years ago
- Python3 wrapper for parallelized gene prediction using Prodigal☆11Mar 3, 2023Updated 3 years ago
- R package for computing alpha and beta contributional diversity metrics☆10May 5, 2023Updated 2 years ago
- A platform for targeted annotation of (meta)genomic and (meta)transcriptomic datasets using HMM sets.☆14Jul 14, 2024Updated last year
- A repository for the lessons and notebooks used for Binder tutorials☆16Oct 24, 2020Updated 5 years ago
- scripts to parse IrysView output☆11Jun 24, 2015Updated 10 years ago
- paprica - PAthway PRediction by phylogenetIC plAcement☆32Apr 16, 2024Updated last year
- ☆14Jan 27, 2026Updated last month
- Protocol for finding informative protein families and then using them to score omic samples☆18Jul 27, 2022Updated 3 years ago
- ☆15Sep 26, 2019Updated 6 years ago
- HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes☆67Mar 2, 2022Updated 4 years ago
- Scripts and resources for analyzing sequence data for select eco-functional genes☆20May 25, 2017Updated 8 years ago
- A Port of SparCC by Yonatan Friedman to Python3☆17Feb 14, 2020Updated 6 years ago
- Hydrocarbon biodegradation gene annotation☆19Jul 14, 2022Updated 3 years ago
- Generate de novo taxonomy of full length 16S rRNA sequences directly from environmental samples☆20Nov 23, 2024Updated last year
- Ensemble binning strategies for combining the output of multiple binning methods.☆22Mar 11, 2023Updated 2 years ago
- ☆57Feb 18, 2026Updated 2 weeks ago
- R and python scripts for correlation-based network analysis☆62May 17, 2020Updated 5 years ago
- ☆26Jun 20, 2023Updated 2 years ago
- Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes☆27Aug 18, 2017Updated 8 years ago
- Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.☆55Jun 14, 2025Updated 8 months ago
- ☆58Mar 14, 2024Updated last year
- Repository containing scripts and files for 16S gene community analysis chapter in Methods in Molecular Biology☆25May 22, 2019Updated 6 years ago
- Phylogenetic and taxonomic analysis for genomes and metagenomes☆82Feb 17, 2016Updated 10 years ago
- StaG Metagenomic Workflow Collaboration☆28Aug 20, 2024Updated last year
- Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!☆178Jan 7, 2026Updated last month
- Nanomotif - a tool for identifying methylated motifs in metagenomic samples☆35Nov 27, 2025Updated 3 months ago
- An R package for microbial community analysis in an environmental context☆67Sep 23, 2020Updated 5 years ago
- Open-source usearch☆132Aug 19, 2025Updated 6 months ago
- Unsupervised Clustering of Environmental Microbial Assemblies Using Coverage and Affinity Propagation☆31May 25, 2021Updated 4 years ago
- Archive: R functions for Analysis of Composition of Microbiomes (ANCOM). Please check our ANCOMBC R package for the most up-to-date ANCOM…☆61Jun 11, 2022Updated 3 years ago
- Convert GTDB taxonomy to NCBI taxdump format☆74Aug 24, 2023Updated 2 years ago
- Repo for course Tools for complex data analysis☆11Jul 15, 2024Updated last year
- Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers☆35Feb 27, 2024Updated 2 years ago
- Phage-Host Interaction Search Tool☆29Jul 8, 2024Updated last year
- Improving genome bins through the combination of different binning programs☆31Jan 30, 2023Updated 3 years ago
- KEGG Module Evaluation Tool☆32Nov 15, 2023Updated 2 years ago
- A robust and fast clustering method for amplicon-based studies☆31Mar 23, 2023Updated 2 years ago
- Remove lambda phage reads from a fastq file☆29Jan 16, 2023Updated 3 years ago