frederic-mahe / swarm
A robust and fast clustering method for amplicon-based studies
☆31Updated last year
Related projects ⓘ
Alternatives and complementary repositories for swarm
- [deprecated] Please use ampvis2☆8Updated 7 years ago
- r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)☆63Updated 11 months ago
- metabaR is an R package to curate and visualise DNA metabarcoding data after basic bioinformatics analyses.☆13Updated last year
- AMPtk: Amplicon ToolKit for NGS data (formally UFITS)☆38Updated last year
- Various customs functions written to enhance the base functions of phyloseq. Most of them are used in the formation "Métagénomique 16S" p…☆33Updated last year
- JAMP - Just Another Metabarcoding Pipeline☆32Updated 2 years ago
- Using ggtree to build phylogenetic trees☆45Updated 2 weeks ago
- Speedy versions of phyloseq functions☆46Updated 7 months ago
- This repository contains CO1 reference sets that can be used with the RDP Classifier, BLAST, or SINTAX to classify COI metabarcode sequen…☆31Updated last year
- Fantaxtic - Nested Bar Plots for Phyloseq Data☆26Updated 4 months ago
- Protist Ribosomal Reference database (PR2) - SSU rRNA gene database☆79Updated last year
- A set of R scripts for the analysis of microbial profiles☆40Updated 6 months ago
- Barcode demultiplex for Illumina I1, R1, R2 fastq.gz files☆31Updated 7 years ago
- MJOLNIR Metabarcoding Joining Obitools & Linkage Networks In R☆17Updated 5 months ago
- functions for analyzing phyloseq data☆26Updated 3 months ago
- The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or t…☆69Updated 2 years ago
- Various functions for analysis of microbial community data☆41Updated 2 years ago
- ☆13Updated this week
- An R package for removing contamination from metabarcoding (e.g., microbiome) datasets post-sequencing☆14Updated last year
- EukRef curation pipeline☆13Updated 3 years ago
- MicrobeCensus estimates the average genome size of microbial communities from metagenomic data☆43Updated 4 years ago
- Scripts and tutorials on how to assemble individual microbial genomes from metagenomes☆80Updated 8 years ago
- ☆50Updated this week
- Compare different differential abundance and expression methods☆50Updated 2 years ago
- Sequence Taxonomic Assignment by Massive Pairwise Alignments☆14Updated last year
- Look Up Guild Information for Fungi in R☆18Updated last year
- ☆69Updated 11 months ago
- Automated pipeline for analyses of fungal ITS from the Illumina☆31Updated 3 months ago
- Utilities for community ecology analysis☆18Updated 4 years ago
- This is a collection of scripts for analyzing mixed 16S/18S amplicon sequences using tools such as qiime2, DADA2, deblur, and bbtools☆28Updated this week