BIFO

RiboDetector

Accurate and rapid RiboRNA sequences Detector based on deep learning

Haploflow

epitope-prediction

Quasimodo

QuasiModo: Assessing viral genomic analysis methods on HCMV strain mixture

epitope-prediction-paper

Data and results for the EpitopeVec paper

AMR_benchmarking

covid-germany-mcmc

SARS-CoV-2 lineage importations and spread are reduced after nonpharmaceutical interventions in phylogeographic analyses

scelestial-paper-materials-devel

The lineage tree reconstruction method based on Steiner tree problem - dataset and test scripts for the paper (development version)

seq2geno

Reproducible and comprehensive sequence analyses for single-species bacterial dataset

ChemLM

corona_lineage_dynamics

SDPlots scripts for the coverage server

mag

Best practice pipeline for assembly and binning of metagenomes based on CAMI2 challenge, adapted from nf-core/mag

Roary

Rapid large-scale prokaryote pan genome analysis

hcv-mds

Neutralization maps for HCV data

AMR_prediction_pipeline

AntigenicTreeTools

Broker4Microbiota

Django App for collection and storage of sequencing orders for the sequencing facility

corona_protein_dynamics

Mutation dynamics analysis of SARS-Cov-2 S-protein based on phylogenetics and statistics

covid-germany-mcmc-one-tree-public

covid-germany-mcmc-phylogeo-tools

A phylogeo-tools for covid-germany-mcmc

fastml

A copy of https://github.com/AidanDelaney/fastml with errors fixed

Haploflow_supplementary

Helper scripts and other supplementary material for Haploflow

lotus

Scripts related to the Lotus japonicus root microbiota manuscript Zgadzaj, Garrido-Oter et al., 2016

ngs_form

phylogeny-of-single-cells

snakemake workflow for the phylogenetic reconstruction of single cell lineages from multiple displacement amplified single cell DNAseq

sankoff

scelestial

snakemake-workflow-univec-removal

A small Snakemake workflow to remove contaminating vector sequences from raw sequencing data using UniVec.

taxprofiler

Highly parallelised multi-taxonomic profiling of shotgun metagenomic data

which_tree

Testing of phylogenetic inference methods