koadman

mauve

A genome alignment and visualization system

AMPHORA

Automated Phylogenomic Inference Pipeline

graphdeconvolution

deconvolution of species & strain genome mixtures in assembly graphs

proxigenomics

Hi-C analysis of heterogeneous samples

strain3C

inference of strain genomes from metagenomic Hi-C data

docker-A5-miseq

a docker container for benchmarking A5-miseq in nucleotid.es

pystan

PyStan: Python interface to Stan

3Creview

analysis & scripts for evaluating 3C & HiC datasets

abacbs2020

longas

long read

mauveAligner

command-line interface software for genome alignment

metapigs

data workflows for pig probiotic & antibiotic trials metagenome analysis

platypusfarm

lab website, software, tutorials, and related material

santa-sim

A forward-time simulator for gene sequences modeling a variety of mutation and selection processes.

angus

Materials for Analyzing Next-Generation Sequencing (ANGUS) course.

assembler-list

List of assemblers to be evaluated.

bananasmoothie

Data and analysis scripts from the KFED microbiome

cqf

A General-Purpose Counting Filter: Counting Quotient Filter

DESMAN

De novo Extraction of Strains from MetAgeNomes

InfinityGenomes

libGenome

Deprecated library for genome sequence file I/O

libMems

a genome alignment library built around seed-and-extend algorithms for maximal exact and unique matches

megahit

MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

meta3Ctools

tools for QC and assembly of metagenomic 3C data

muscle

library refactorization of the MUSCLE aligner by Robert Edgar

primalscheme

a tool for designing primer panels for multiplex PCR.

repeatoire

constructs local multiple alignments of repeat families

sgEvolver

The simple genome evolver

TheEvilAnalysis

repository for reanalysis of milk microbiome data