leoisl

amygda

Automated Mycobacterial Growth Detection Algorithm, funded by NIHR Oxford Biomedical Research Centre

GCP

Genotype confidence percentile header-only c++ implementation

racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads

viridian_visualisations

CAP

Implementation of the algorithm to solve the Chain Alignment Problem (CAP) and the three heuristics for the Multiple Chain Alignment Problem (MCAP) in C

cytoscape_on_cluster

cyvcf2

cython + htslib == fast VCF and BCF processing

docker_recipes

easy_bwast

Command line BLAST made-easy

gatb-core

Core library of the Genome Analysis Toolbox with de-Bruijn graph

head_to_head_pipeline

Snakemake pipeline to run analysis for the Illumina vs. Nanopore comparison.

libarchive

Multi-format archive and compression library

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

MobMess

mugardp

mugarteam

mugarteam

ortho_lfc_parser

pandora_dev_support

Pandora development support scripts/tools/etc

pandora_gene_distance

perf-ninja

This is an online course where you can learn and master the skill of low-level performance analysis and tuning.

python_training_1

Python training 1: refactoring code into classes, unit testing, mocking

random

random stuff

Scoary

Pan-genome wide association studies

snakemake-lsf

Cookiecutter for snakemake LSF profile

spoa

SIMD partial order alignment tool/library

subsampler

tbpore

Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data

variant_callers_pipeline

varifier

Variant call verification

vcf_consensus_builder

Build a consensus sequence from a VCF and reference sequence masking low and no coverage positions