knights-lab

BURST

An ultrafast optimal aligner for mapping large NGS data to large genome databases.

SHOGUN

SHallow shOtGUN profiler

MLRepo

shi7

Auto-parameterizing QC Pipeline for Illumina sequencing runs

dietstudy_analyses

Food_Tree

USDA Nutrition codes Tree

LMdist

LMdist is an unsupervised algorithm for correcting oversaturated pairwise distance and dissimilarity measures. Compatible with any pairwise beta diversity measure, LMdist will uncover underlying environmental gradients and resolve arches/horseshoes in ordination.

IMP_analyses

immigrant microbiome project related analyses

UTree

K-mer searching with trees

climate-trace-shipping

ermin-standards

Emissions Report Minimum INformation (ERMIN) Standards

aKronyMer

Ultrafast genome- and dataset-scale distance matrix and phylogenetic tree creation

analysis_SHOGUN

Analysis scripts and code for reproducing the analysis for the SHOGUN paper

conda-recipes

Conda recipes for the knights lab

DOJO

kafan

Lossless data compression codec specialized for sequence data

NINJA-utils

Reusable classes and configurations for easy Python package development.

q2-ninja-ops

QIIME2 Plugin for NINJA-OPS

analysis_italy

analysis_tree

BetaDiv

Materials and analyses for "Microbiome beta diversity analyses and visualization." A discussion of beta diversity analysis methods, factors we must consider in each step, and how we might better use these methods in forthcoming microbiome research.

dietstudy

Diet Study

douc_gut_sites

Microbiome of red-shanked douc gut sites

foodworks

Experimenting with Bayesian Networks for predicting day-to-day microbiome fluctuations

helix

Short scripts for use within the knights-lab

IMP-Open-Ref

Open Ref BURST with IMP data

knights-lab.github.io

Knights Lab website via Github pages

MAGICstudy

The Microbiome, Antibiotics, and Growth Infant Cohort associated analyses.

megaperm

Two-group, two-timepoint non-parametric permutation-based significance testing allowing for uneven repeated sampling (whew!)

type_1