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neo-pipeline

SLURM pipeline for processing neo aDNA samples

new-iron-20190323-pipelines

omicron-neutralization-paper

antigenic cartography and antibody landscapes related code and figures for the paper Analysis of SARS-CoV-2 Omicron Neutralization Data up to 2022-28-01

parvo-2018

FASTA alignments and BEAST2 XML files for the PNAS paper "Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans"

parvo-blastn-pipeline-spec

phylo-color

Add color information to nodes in a phylogenetic tree

puffinosis-diamond-bacterial

A slurm-pipeline specification and scripts for running Puffinosis reads against the NCBI bacterial refseq

puffinosis-diamond-viral

A slurm-pipeline specification and scripts for running Puffinosis reads against the NCBI viral refseq

py3seq

Python wrapper for the 3seq recombination detection algorithm

pymds

Metric multidimensional scaling in python

racmacs

Racmacs R package for performing antigenic cartography https://acorg.github.io/Racmacs

receptor-binding-sites

Depositing information and structures related to location of receptor binding sites in various HA structures

recombination

Experiments to investigate the effect of recombination on ML trees

repeated-vaccination

Simple code for Bayesian work on lineage switching and Influenza B vaccines

richard-pipeline

richard-pipeline-bacteria

roessler_netzl_et_al2022

Code repository for "BA.2 and BA.5 omicron differ immunologically from both BA.1 omicron and pre-omicron variants" by Roessler, A., Netzl, A., et al.

seqdb

Set of tools to build and query sequence database

seqdb-3

Set of tools to build and query sequence database v3

seqdb-make-tree-signature-page

Set of tools to build, query sequence database and to generate phylogenetic trees.

seqgen

Python code for generating sequences in FASTA format

signature-page

Programs to import phylogenetic tree and draw it on a tree or signature page

simple-bwa-blastn-bowtie2-experiments

simple-slurm-loop

Simple shell scripts to run a looping job on SLURM

slurm-pipeline

A Python class for scheduling SLURM jobs

sofia-blastx-pipeline

A slurm-pipeline specification and scripts for processing Sofia data

sofia-pipeline

A pipeline for Sofia P

ssm-report

Documentation and scripts for SSM and TCs report preparation

standard-raxml

thijs-labels

Label generator for Thijs Kuiken