frederic-mahe / swarmLinks
A robust and fast clustering method for amplicon-based studies
☆31Updated 2 years ago
Alternatives and similar repositories for swarm
Users that are interested in swarm are comparing it to the libraries listed below
Sorting:
- r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)☆67Updated last year
- [deprecated] Please use ampvis2☆8Updated 7 years ago
- Various customs functions written to enhance the base functions of phyloseq. Most of them are used in the formation "Métagénomique 16S" p…☆33Updated 3 months ago
- Speedy versions of phyloseq functions☆47Updated last year
- Barcode demultiplex for Illumina I1, R1, R2 fastq.gz files☆31Updated 8 years ago
- AMPtk: Amplicon ToolKit for NGS data (formally UFITS)☆38Updated last year
- EukRef curation pipeline☆13Updated 4 years ago
- functions for analyzing phyloseq data☆28Updated 4 months ago
- This repository contains CO1 reference sets that can be used with the RDP Classifier, BLAST, or SINTAX to classify COI metabarcode sequen…☆32Updated 2 years ago
- Sequence Taxonomic Assignment by Massive Pairwise Alignments☆14Updated last year
- Using ggtree to build phylogenetic trees☆47Updated 7 months ago
- Parse NCBI taxonomy and accessions to find taxonomic assignments☆76Updated 3 months ago
- A set of R scripts for the analysis of microbial profiles☆41Updated last year
- Various functions for analysis of microbial community data☆45Updated 2 years ago
- Protist Ribosomal Reference database (PR2) - SSU rRNA gene database☆81Updated 2 weeks ago
- Automated pipeline for analyses of fungal ITS from the Illumina☆31Updated last month
- Fantaxtic - Nested Bar Plots for Phyloseq Data☆31Updated 11 months ago
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆88Updated last month
- The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or t…☆71Updated 2 years ago
- metabaR is an R package to curate and visualise DNA metabarcoding data after basic bioinformatics analyses.☆15Updated 4 months ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated 2 years ago
- Tools for visualising microbial community amplicon data☆67Updated 2 months ago
- An R package for removing contamination from metabarcoding (e.g., microbiome) datasets post-sequencing☆16Updated last year
- ☆12Updated last year
- Compare different differential abundance and expression methods☆51Updated 3 years ago
- JAMP - Just Another Metabarcoding Pipeline☆36Updated 3 years ago
- diversity estimation under ecological networks☆83Updated 2 months ago
- Reproducible Analyses accompanying DADA2 + PacBio Manuscript☆32Updated 4 years ago
- Sydney Phylogenetics Workshop☆62Updated this week
- ☆16Updated this week