Pinned Repositories
abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
ACE2
Supporting material and code for primate ACE2 project
AliTV
Visualize whole genome alignments as linear maps
asqcan
Pipeline for bacterial genome assembly, quality control and annotation
BactDating
Bayesian inference of ancestral dates on bacterial phylogenetic trees
base_changer
Changes bases in a fasta file at user specified positions
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.
ClonalFrameML
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
clusterDbAnalysis
ITEP - Integrated Toolkit for Exploration of microbial Pan-genomes
Comparative_Genomics
Micro 612 genomics workshop
kdbrumfield's Repositories
kdbrumfield/abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
kdbrumfield/ACE2
Supporting material and code for primate ACE2 project
kdbrumfield/asqcan
Pipeline for bacterial genome assembly, quality control and annotation
kdbrumfield/BactDating
Bayesian inference of ancestral dates on bacterial phylogenetic trees
kdbrumfield/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.
kdbrumfield/deviaTE
Python tool for the analysis and visualization of mobile genetic elements
kdbrumfield/environmental_cholera_haiti
Evidence of Environmental Evolution of Toxigenic Vibrio cholerae in Aquatic Reservoirs
kdbrumfield/fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
kdbrumfield/gotree
Gotree
kdbrumfield/iMGEins
kdbrumfield/kaiju
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
kdbrumfield/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"
kdbrumfield/Linux-Magic-Trackpad-2-Driver
kdbrumfield/MGEfinder
A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
kdbrumfield/MGERT
Mobile Genetic Elements Retrieving Tool
kdbrumfield/modeltest
Best-fit model selection
kdbrumfield/mustache
A flexible tool to identify mobile genetic elements and their sites of insertions from short-read whole-genome sequencing data.
kdbrumfield/pathogen-informatics-training
kdbrumfield/pop_gen
Population genetic scripts
kdbrumfield/Public
Short scripts used for Assembly and Annotation
kdbrumfield/pySCA
A python implementation of the Statistical Coupling Analysis (SCA)
kdbrumfield/RaGOO
Fast Reference-Guided Scaffolding of Genome Assembly Contigs. RagTag, the successor to RaGOO, is now available here: https://github.com/malonge/RagTag
kdbrumfield/RagTag
A fast reference-guided genome assembly scaffolder
kdbrumfield/Scaffold_builder
Combining de novo and reference-guided assembly with Scaffold_builder
kdbrumfield/snpiphy
An automated snp phylogeny pipeline
kdbrumfield/sourcetracker2
SourceTracker2
kdbrumfield/SourceTracker2-diagnostics
Add-on diagnostic tool for SourceTracker2
kdbrumfield/sunbeam
A robust, extensible metagenomics pipeline
kdbrumfield/Vibrio_genomics
kdbrumfield/vr-codebase
The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute