Lisa Jones's repositories
bactmap
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
biobash
A collection of bash scripts for bioinformatics
dryad
Dryad is a pipeline to construct reference free core-genome or SNP phylogenetic trees for examining prokaryote relatedness in outbreaks.
github-slideshow
A robot powered training repository :robot:
introducing-python
An introduction to Python
IntroToDataScience
GitHub Repository to accompany my YouTube series of videos on Introductory Data Science using R.
mumps
Nextstrain build for mumps virus
mumps-seq
Protocols for sequencing mumps viruses
oneliners
Useful bash one-liners for bioinformatics.
PythonForBioinformatics
This repository will be helpful to start using python for your Bioinformatics projects.
SARS-CoV-2_Sequencing
A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.
sarscov2recombinants
Scan SARS-SoV-2 sequences for potential recombinants
seqtk
Toolkit for processing sequences in FASTA/Q formats
staphb_toolkit
Python Toolkit for using containerized programs in either Singularity or Docker
TB_molecular_epidemiology
Algorithms for TB molecular epidemiology analysis
tormes
Making whole bacterial genome sequencing data analysis easy
viral-pipelines
viral-ngs: complete pipelines
wdl
Workflow Description Language - Specification and Implementations