Pinned Repositories
3Creview
analysis & scripts for evaluating 3C & HiC datasets
abacbs2020
AMPHORA
Automated Phylogenomic Inference Pipeline
docker-A5-miseq
a docker container for benchmarking A5-miseq in nucleotid.es
graphdeconvolution
deconvolution of species & strain genome mixtures in assembly graphs
longas
long read
mauve
A genome alignment and visualization system
proxigenomics
Hi-C analysis of heterogeneous samples
pystan
PyStan: Python interface to Stan
strain3C
inference of strain genomes from metagenomic Hi-C data
koadman's Repositories
koadman/mauve
A genome alignment and visualization system
koadman/AMPHORA
Automated Phylogenomic Inference Pipeline
koadman/graphdeconvolution
deconvolution of species & strain genome mixtures in assembly graphs
koadman/proxigenomics
Hi-C analysis of heterogeneous samples
koadman/strain3C
inference of strain genomes from metagenomic Hi-C data
koadman/docker-A5-miseq
a docker container for benchmarking A5-miseq in nucleotid.es
koadman/pystan
PyStan: Python interface to Stan
koadman/3Creview
analysis & scripts for evaluating 3C & HiC datasets
koadman/abacbs2020
koadman/longas
long read
koadman/mauveAligner
command-line interface software for genome alignment
koadman/metapigs
data workflows for pig probiotic & antibiotic trials metagenome analysis
koadman/platypusfarm
lab website, software, tutorials, and related material
koadman/santa-sim
A forward-time simulator for gene sequences modeling a variety of mutation and selection processes.
koadman/angus
Materials for Analyzing Next-Generation Sequencing (ANGUS) course.
koadman/assembler-list
List of assemblers to be evaluated.
koadman/bananasmoothie
Data and analysis scripts from the KFED microbiome
koadman/cqf
A General-Purpose Counting Filter: Counting Quotient Filter
koadman/DESMAN
De novo Extraction of Strains from MetAgeNomes
koadman/InfinityGenomes
koadman/libGenome
Deprecated library for genome sequence file I/O
koadman/libMems
a genome alignment library built around seed-and-extend algorithms for maximal exact and unique matches
koadman/megahit
MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
koadman/meta3Ctools
tools for QC and assembly of metagenomic 3C data
koadman/muscle
library refactorization of the MUSCLE aligner by Robert Edgar
koadman/primalscheme
a tool for designing primer panels for multiplex PCR.
koadman/repeatoire
constructs local multiple alignments of repeat families
koadman/sgEvolver
The simple genome evolver
koadman/TheEvilAnalysis
repository for reanalysis of milk microbiome data