Pinned Repositories
bioinf-scripts
Farmpy
Python3 package to handle job submission to a compute farm
ftep
ENA metadata queries
minos
Variant call adjudication
pacbio-14-nctc-assemblies
14 NCTC samples for testing PacBio assemblers
pathogen-informatics-training
Scaffolder-evaluation
Wrapper scripts to run genome assembly scaffolding tools and scripts to analyse the output for accuracy.
slurmzy
Slurm wrapper scripts
ushonium
usher + taxonium
varifier
Variant call verification
martinghunt's Repositories
martinghunt/tna
martinghunt/slurmzy
Slurm wrapper scripts
martinghunt/bioinf-scripts
martinghunt/ushonium
usher + taxonium
martinghunt/varifier
Variant call verification
martinghunt/ftep
ENA metadata queries
martinghunt/minos
Variant call adjudication
martinghunt/mykrobe
Cli tools for Mykrobe atlas and Mykrobe predictor
martinghunt/AllTheBacteria
Follow up to Grace Blackwell's 661k dataset, for 2023
martinghunt/ariba
Antibiotic Resistance Identification By Assembly
martinghunt/clockwork
CRyPTIC data processing pipelines
martinghunt/cluster_vcf_records
Python package to cluster VCF records. Used by gramtools and minos
martinghunt/cortex
reference free variant assembly
martinghunt/covid-truth-eval
Evaluate accuracy of covid assemblies where truth is available
martinghunt/cylon
Virus assembler from amplicon sequencing reads
martinghunt/gat
github actions testing
martinghunt/gramtools
Genome inference from a population reference graph
martinghunt/mccortex
Cortex on steroids: for larger populations with better assembly
martinghunt/minos-paper-benchmarking
martinghunt/mykrobe-lineage-test
Test species and lineage calls made by mykrobe
martinghunt/py-cortex-api
Python API for cortex
martinghunt/read-it-and-keep
Read contamination removal
martinghunt/rtd-test
martinghunt/sprog
Species Probes Generator
martinghunt/test-b
test repo a
martinghunt/test-c
test repo b
martinghunt/tnahelper
TNA helper binary
martinghunt/triphecta
martinghunt/viridian
martinghunt/viridian-paper
Scripts for the viridian paper