Pinned Repositories
VATK
Virus Analysis Tool Kit
weeSAM
Script for parsing SAM/BAM files for coverage statistics
btctools
Beyond the consensus NGS tools
DiversiTools
Tool for analysing viral diversity from High Throughput Sequencing
PrepPhyloViz
preparing files for phyloviz software
Sequence-manipulation
A range of different perl scripts for manipulating sequences, conducting alignments, consensus sequences, changing formats
ViCTree
An automated framework to aid taxonomic classification of viruses
viral-bioinformatics-training
Material for the GECO viral bioinformatics training, Manila, Philippines
josephhughes's Repositories
josephhughes/Sequence-manipulation
A range of different perl scripts for manipulating sequences, conducting alignments, consensus sequences, changing formats
josephhughes/DiversiTools
Tool for analysing viral diversity from High Throughput Sequencing
josephhughes/btctools
Beyond the consensus NGS tools
josephhughes/ViCTree
An automated framework to aid taxonomic classification of viruses
josephhughes/viral-bioinformatics-training
Material for the GECO viral bioinformatics training, Manila, Philippines
josephhughes/cvrProject
Cataloguing SRA data into Shiny App
josephhughes/DIG
Masters Project for Benchmarking pipeline for detecting Defective interfering particles
josephhughes/GenRefSeq
This pipeline and scripts allows for selected sequences to be collected, which span the virus/genus diversity for a given taxonomic ID, which in turn can be used in reference-based assembly projects
josephhughes/Master-Project
Repository for SRA characterisation, classifier benchmarking, custom database creation and assembly of the Rattus Norvegicus viromes
josephhughes/MasterProject
Script for testing cophylogenetic reconstruction tools
josephhughes/Tutorials
Different bioinformatic tutorials for analysing sequence data and other type of bioinformatic data
josephhughes/baltic
baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).
josephhughes/beastgenpy
josephhughes/blogs
Jupyter notebooks that support my graph data science blog posts at https://bratanic-tomaz.medium.com/
josephhughes/CoPi
Pipeline for detecting coinfection of SARS-CoV-2 variants.
josephhughes/covid-19
A collection of work related to COVID-19
josephhughes/ete
Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
josephhughes/grapevine-PHL
josephhughes/HCMVmut
Identifying low frequency mutations in the HCMV genome
josephhughes/host_depletion_metagenomics
josephhughes/LASV_Sample_Classification
Collection of scripts and pipelines to process Illumina reads from LASV positive samples into taxonomically classified contigs.
josephhughes/MasCMV_Transcriptomics
A collection of scripts and Snakemake pipelines used in the characterisation of the Mastomys natalaensis cytomegalovirus (MasCMV) transcriptome.
josephhughes/Masters_project
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josephhughes/MERS-Cases
josephhughes/nimagen_snakemake
A nimagen workflow implemented in snakemake.
josephhughes/pango-designation
Repository for suggesting new lineages that should be added to the current scheme
josephhughes/seq-div
Suit of scripts for diversity measurements
josephhughes/TINAF
Scripts for processing nCoV Illumina reads, metadata from GISAID and reconstructing phylogeny
josephhughes/tree-manip
Collection of scripts for dealing with phylogenies
josephhughes/wossvc_hiv