The Hildebrand Lab is a research group based at the Quadram Institute and Earlham Institute in Norwich, UK.

We use metagenomics and develop associated bioinformatics algorithms to explore ecosystems from a global scale to the individual human gut microbiome.

For more detail see falk.science.

We have developed a number of pipelines combining multiple pieces of software. These are kept by member of the group on their personal accounts. Below are links to pipelines developed in the group.

• LotuS3 (github) 16S/18S/ITS & other target amplicon sequencing pipeline for long & short read sequencing.

• MG-TK (github) MetaGenomic ToolKit, pipeline handling end-to-end processing of metagenomes.

• BM-TK (github) Batch prediction of base modfication for PacBio data from kinetics information.

Software developed by members of the group are kept on their personal github accounts. Below are links to software developed in the group.

• adhesiomeR (github) (web) Detect adhesion genes in E. coli, also available as a webserver.

• cvanmf (github) (conda) (docs) Bicrossvalidated NMF clustering of data sets, with nextflow pipeline for application to large datasets.

• enterosignatures (web) Webserver to quantify enterosginatures in gut microbiomes.

• protal (github) Alignment-based based strain-level metagenomic profiler.

• benchpro (github) Evaluation suite for taxonomic profiler performance.

• varkit (github) k-mer-based strain-level metagenomic profiler.

• RTK2 (github) (conda) Matrix operations on large metagenomic gene catalogues.

• LCA (github) (conda) Least common ancestor taxonomy calculations.

• SDM (github) (conda) Demultiplexing and read quality filtering software.

• MSAFix (github) Fixing frameshift errors in MSAs.

• canopy2 (github) (conda) Binning of metagenomic gene catalogues.

• clusterMAGs (github) Binning of metagenomic gene catalogues.

• rdCover (github) Read coverage of genes, genomes etc.

• KSGP (github) 16S Database of Archaea with deeper taxonomic resolution and GTDB format.

Some software or pipelines have been updated, below are links to previous versions.

• RTK (github) (conda) (cran) Rarefaction and diversity analysis. Updated in RTK2.

• LotuS2 (github) (web) (conda) 16S/23S/ITS amplicon sequencing pipeline for illumina and PacBio sequences, supersed by LotuS3.

• LotuS (web) Amplicon sequencing pipelines. Superseded by LotuS2.

• MATAFILER (github) Metagenomics pipeline, replaced by MG-TK.