Home

Welcome to the SLIM wiki

In these pages you will find tutorials for beginners and programmers and details on each module.

Tutorials

• Start with SLIM (In progress)
• How to write a module
• How to write a module II: ASHURE example, concept and installation
• How to write a module II: ASHURE example, Module scripts

List of the modules:

Demultiplexing / sample grouping

• Double Tag Demultiplexing (DTD)
• Wildcard creator

Paired-end joiners

• Pandaseq joining
• Casper
• Mergepair vsearch

Chimeras

• Chimera Vsearch

ASVs inference / OTUs clustering

• DADA2
• Clustering vsearch
• SWARM v2
• SWARM v3
• OPTICS

Assignment

• fasta - vsearch
• OTU table - vsearch
• OTU/ASV table - IDTAXA
• FASTA - IDTAXA

Post-processing

• LULU post clustering

Nanopore pipeline

• ASHURE
• MSI

Utils

• Dereplication
• Basic FASTA filtering
• Basic OTU filtering
• FASTA merging
• FASTQ to FASTA
• CHOPPER