drhchen

adegenet

adegenet: a R package for the multivariate analysis of genetic markers

RiDiCulousFilter

Filter sequences based on a variety of conditions

BactSNP

KMC

Fast and frugal disk based k-mer counter

kounta

🧮 🔢 Generate multi-sample k-mer count matrix from WGS

kmersGWAS

A library for running k-mers based GWAS

binary_tree

To convert gene-presence-absence matrix into multi fasta alignment

orthocounts2bin

A script to get from Orthogroups.GeneCount.tsv to a gene presence/absence binary alignment.

GenAPI

Gene Absence Presence Identification tool.

matrix_converter

Small matrix converter tool for my design project

treeWAS

treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes

ClonalFrameML

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

dsk

k-mer counting software

ISseeker

A tool to find Insertion Sequences by blasting their flanking sequences against a reference.

gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

mlst

:id: Scan contig files against PubMLST typing schemes

AMR_ML

LS-BSR

Large scale Blast Score Ratio (BSR) analysis

plasmidtron

Assembling the cause of phenotypes and genotypes from NGS data

seqfilter

Filter fasta/fastq(.gz) files by ID and/or sequence length

SeqFilter

Versatile FASTA/FASTQ sequence file analysis and modification tool

Roary

Rapid large-scale prokaryote pan genome analysis

Scoary

Pan-genome wide association studies

bac-genomics-scripts

Collection of scripts for bacterial genomics

parsnp

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.

bacterial_GWAS_tutorial

Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop