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3creview

analysis & scripts for evaluating 3C & HiC datasets

abacbs2020

amphora

Automated Phylogenomic Inference Pipeline

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

docker-a5-miseq

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

graphdeconvolution

deconvolution of species & strain genome mixtures in assembly graphs

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

longas

long read

mauve

A genome alignment and visualization system

mauvealigner

command-line interface software for genome alignment

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

metapigs

data workflows for pig probiotic & antibiotic trials metagenome analysis

muscle

library refactorization of the MUSCLE aligner by Robert Edgar

platypusfarm

lab website, software, tutorials, and related material

primalscheme

a tool for designing primer panels for multiplex PCR.

proxigenomics

Hi-C analysis of heterogeneous samples

pystan

PyStan: Python interface to Stan

repeatoire

constructs local multiple alignments of repeat families

santa-sim

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

sgevolver

The simple genome evolver

strain3c

inference of strain genomes from metagenomic Hi-C data

theevilanalysis

repository for reanalysis of milk microbiome data