LotuS2
Updated LotuS pipeline, Dada2 + Unoise clustering, improved speed, LULU and crosstalk postprocessing, offtarget removal, updated tax assignment, better phylogenies and a more rounded user experience.
Available from lotus2.earlham.ac.uk
LotuS
Fast, easy-to-use and highly accurate amplicon sequencing pipeline. Choose between several highly accurate OTU calling algorithms, choose from general or spezialized databases to annotate these taxonomically and create a phylogeny of OTUs - all in on single command.
Available with self-installer from http://psbweb05.psb.ugent.be/lotus/
MATAFILER
Pipeline to process metagenomic data from raw reads to taxonomic and functional abudnance matrices. However, the way is the quest and MATAFILER offers the assembly-dependent (gene catalog) and assembly-independent (direct mapping to appropriate databases) workflow. Both are useful in specific situations, e.g. the highly complex soil metagenome often cannot be properly assembled and gene catalog based methods will struggle.
RTK
RTK (rarefaction toolkit) provides fast and scalable rarefaction and diversity estimation for numerical ecology data (e.g. species abundance tables). RTK uses significantly (~100x) less memory while being ~10x faster than competing software. Accessible through R interface - install.package(“rtk”) - or C++ binary:
KSGP
KSGP 16S database for Bacteria, Eukaryotes and Archaeae. Has a significantly higher taxonomic coverage for Archaea and uses GTDB conform taxonomy. Fully integrated with LotuS2.
Database webpage:
AdhesiomeR
AdhesiomeR can be used to classify adhesion related genes in E coli genomes. Available in R or through webserver to directly upload and explore genomes:
https://adhesiomer.quadram.ac.uk/