We develop practical, open-source pipelines, reference resources and analysis tools for amplicon sequencing, shotgun metagenomics, genome reconstruction and community ecology. Our software is designed to be useful beyond a single lab, with source code and documentation available through each project’s repository.
Pipelines
These pipelines coordinate read processing and established third-party methods. Their repositories document required inputs, configuration, outputs and software dependencies.
Processes marker-gene amplicons, including 16S, 18S and ITS data. A run can use DADA2, UPARSE, UNOISE3, CD-HIT or VSEARCH to infer OTUs or ASVs, then assign taxonomy and produce abundance tables, representative sequences, run logs and method-specific citation files.
944 Bioconda downloads
2 GitHub stars
Documentation and code LotuS2 methods paper
Processes raw shotgun metagenomes on Linux or high-performance computing systems. It provides assembly-dependent analysis for communities with recoverable assemblies, assembly-independent taxonomic and functional profiling for highly complex samples, hybrid assembly support and mapping to defined reference targets.
0 GitHub release downloads
4 GitHub stars
Documentation and codeTools & resources
Profiling, taxonomic reference data, genome processing, statistical modelling, phylogenetic quality control and visualisation.
Profiling
Uses paired-end short reads and a database of universal single-copy marker genes to profile bacterial species. It retains marker alignments across samples for reference-guided, within-species comparison and phylogeny. The current method and benchmarks are described in a 2026 preprint.
1,468 Bioconda downloads
16 GitHub stars
Documentation and code Read the preprintStatistical modelling
Applies bicross-validation to select the rank of a non-negative matrix factorisation, then evaluates the stability of the resulting signatures. It accepts numerical feature-by-sample matrices and includes analysis and visualisation functions for interpreting the decomposition.
715 Bioconda downloads
5 GitHub stars
Documentation and code Read the methods paperReference database
A curated small-subunit ribosomal RNA reference for archaeal community analysis, developed with collaborators at UEA. It combines GTDB-conformant taxonomy with cleaned prokaryotic and eukaryotic references; the lab contributed its integration with LotuS2. In benchmark datasets, KSGP 3.1 improves class- and order-level archaeal assignment over the tested alternatives.
Open the database Read the paperGenome analysis
Searches Escherichia coli genomes, pangenomes or metagenomic gene catalogues for adhesin genes by BLAST. Its curated database contains 525 genes grouped into 102 adhesin systems, with a strict mode for known genes and configurable relaxed thresholds for putative homologues. It describes an adhesin repertoire; it does not by itself predict pathogenicity.
0 GitHub release downloads
4 GitHub stars
Documentation and code Read the paperRead processing
A compiled utility used within the LotuS workflows for demultiplexing, quality filtering, primer handling and dereplication of amplicon reads. Configuration records the filtering decisions applied to each run.
77,364 Bioconda downloads
6 GitHub stars
Documentation and codeNumerical ecology
Performs repeated rarefaction of large abundance matrices and calculates alpha- and beta-diversity summaries. It is available through an R interface and as a compiled command-line program.
44,561 CRAN downloads
18 GitHub stars
Documentation and code Read the paperTaxonomy
Assigns sequences to the least common taxonomic ancestor supported by database hits. It is used as a taxonomic assignment component in the group's amplicon workflows rather than as a biological interpretation on its own.
26,977 Bioconda downloads
0 GitHub stars
Documentation and codeGenome grouping
A compiled program for grouping metagenome-assembled genomes into metagenomic species using a gene catalogue and universal marker genes. The repository provides the implementation and build instructions.
0 GitHub release downloads
1 GitHub star
Documentation and codeAlignment quality control
Checks and cleans nucleotide or amino-acid multiple-sequence alignments. It can remove poorly supported regions and conservatively correct technical gap-placement offsets in coding alignments without inventing missing nucleotides; true biological frameshifts require a frameshift-aware aligner.
0 GitHub release downloads
1 GitHub star
Documentation and codeBase modifications
A Nextflow workflow for PacBio HiFi BAM files containing polymerase-kinetics tags. It checks inputs, calls 6mA, 5mC and 5hmC through jasmine and can export high-confidence calls to tables.
0 GitHub release downloads
2 GitHub stars
Documentation and codeVariant consensus
Builds haploid, community-aware bacterial consensus contigs and annotated gene sequences from a metagenomic reference, VCF calls, depth tracks and a GFF annotation. Filtering uses explicit depth, allele-support and quality criteria rather than the VCF genotype alone.
0 GitHub release downloads
1 GitHub star
Documentation and codeMarker discovery
A Nextflow workflow for finding clade-specific marker-gene families across GTDB genomes. It clusters proteins, scores in-clade and out-of-clade prevalence at successive taxonomic ranks and emits a nucleotide marker database from species representatives.
0 GitHub release downloads
0 GitHub stars
Documentation and codeBenchmarking
Compares taxonomic-profiler output against known community composition and accepts GTDB-style taxonomy. The repository is the current source for supported formats and metrics.
0 GitHub release downloads
2 GitHub stars
Documentation and codePhylogeny
An interactive viewer for phylogenetic trees with sample metadata and summary values displayed alongside the tips.
0 GitHub release downloads
0 GitHub stars
Documentation and codeCommunity signatures
Estimates the weights of the five published enterosignatures from a GTDB genus-abundance table. The browser application and command-line workflow apply the fixed model described by Frioux and colleagues.
0 GitHub release downloads
0 GitHub stars
Documentation and code Open the calculator Read the paperGene catalogues
Clusters co-abundant genes from large metagenomic gene catalogues into groups for subsequent genome and community analysis.
4 tagged versions
0 GitHub stars
Documentation and codeSoftware archive
These repositories are retained for established analyses and reproducibility, but should generally be considered deprecated. Consult their documentation before reuse.
The published predecessor of LotuS3. It processes short- and long-read amplicons through demultiplexing, filtering, OTU/ASV inference, taxonomic assignment and standard downstream outputs.
69,982 Bioconda downloads
54 GitHub stars
Documentation and code Read the paperThe original Less OTU Scripts pipeline for amplicon-sequence processing, described in the 2014 methods paper. LotuS3 is the current implementation.
Historic download count unavailable
Read the LotuS paperThe earlier shotgun-metagenomics workflow for assembly, genome reconstruction and taxonomic and functional profiling. It is retained here for reference.
0 GitHub release downloads
7 GitHub stars
Open the archived repository
An earlier toolkit for processing shotgun metagenomes into taxonomic and functional abundance data. It is retained here for reference.
0 GitHub release downloads
8 GitHub stars
Open the repositoryFor project-specific support, documentation or collaboration ideas, start with the repository and contact the lab when a conversation would help.
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