MrOlm

drep

Rapid comparison and dereplication of genomes

inStrain

Bioinformatics program inStrain

covid19_population_genomics

Analysis of the population diversity of SARS-CoV-2 within and between individual patients

tRep

Quickly get the taxonomy of a genome

pipeCoverage

Quickly calculate coverage of sequences in a .sam file while retaining breadth information

bacterialEvolutionMetrics

Scripts in support of publication

drep_instrain_tutorial

Tutorial for dRep and inStrain. Made for EBAME7

MIGSeq_code

Code supporting the publication "Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Healthy Human Gut Microbiome"

VICA

Identifying VIral and Circular content in metAgenomes

InfantEukaryotes

Notebooks supporting the publication "Strain-level overlap between infant and hospital fungal microbiomes revealed through de novo assembly of eukaryotic genomes from metagenomes"

nf-genomeresolvedmetagenomics

A nextflow pipeline to perform genome resolved metagenomics

ZenodoREADME

README for Zenodo archive associated with publication Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes

glrestore

Easily restore objects from AWS glacier from the command line using python

scripts

Miscellaneous scripts

aegea

Amazon Web Services Operator Interface

artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus

bioconda-recipes

Conda recipes for the bioconda channel.

iRep

scripts for estimating bacteria replication rates based on population genome copy number variation

Kleborate

metaphlan-nf

Quantify microbial abundance from whole-genome shotgun sequencing data

modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

mrolm.github.io

Matthew Olm Website

nextflow-tutorial

Nextflow training material for introductory tutorial

Public-Scripts

py_sa

Interact with aegea and s3 through python

sars_cov_2_inversion

Reproducible analyses for analyzing proposed rare genomic inversions in SARS-COV-2

strainProfiler

Program to analyze strain-level diversity within a population

VirFinder

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data