Kyle Brumfield's repositories
sunbeam
A robust, extensible metagenomics pipeline
fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Bracken
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
RaGOO
Fast Reference-Guided Scaffolding of Genome Assembly Contigs. RagTag, the successor to RaGOO, is now available here: https://github.com/malonge/RagTag
RagTag
A fast reference-guided genome assembly scaffolder
ACE2
Supporting material and code for primate ACE2 project
BactDating
Bayesian inference of ancestral dates on bacterial phylogenetic trees
environmental_cholera_haiti
Evidence of Environmental Evolution of Toxigenic Vibrio cholerae in Aquatic Reservoirs
gotree
Gotree
kaiju
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
SourceTracker2-diagnostics
Add-on diagnostic tool for SourceTracker2
modeltest
Best-fit model selection
King_et_al_2019
Script(s) used in publication of King et al, 2019 "A new high throughput sequencing assay for characterising the diversity of natural Vibrio communities and its application to a Pacific oyster mortality event"
sourcetracker2
SourceTracker2
MGEfinder
A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
MGERT
Mobile Genetic Elements Retrieving Tool
deviaTE
Python tool for the analysis and visualization of mobile genetic elements
pySCA
A python implementation of the Statistical Coupling Analysis (SCA)
mustache
A flexible tool to identify mobile genetic elements and their sites of insertions from short-read whole-genome sequencing data.
asqcan
Pipeline for bacterial genome assembly, quality control and annotation
snpiphy
An automated snp phylogeny pipeline
pop_gen
Population genetic scripts
vr-codebase
The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute
Public
Short scripts used for Assembly and Annotation
Scaffold_builder
Combining de novo and reference-guided assembly with Scaffold_builder