mrolm Goto Github PK

aegea

Amazon Web Services Operator Interface

artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus

bacterialevolutionmetrics

Scripts in support of publication

bioconda-recipes

Conda recipes for the bioconda channel.

covid19_population_genomics

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

drep

Rapid comparison and dereplication of genomes

drep_instrain_tutorial

Tutorial for dRep and inStrain. Made for EBAME7

glrestore

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

infanteukaryotes

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

instrain

Bioinformatics program inStrain

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

migseq_code

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

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

nf-genomeresolvedmetagenomics

A nextflow pipeline to perform genome resolved metagenomics

pipecoverage

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

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

scripts

Miscellaneous scripts

strainprofiler

Program to analyze strain-level diversity within a population

trep

Quickly get the taxonomy of a genome

vica

Identifying VIral and Circular content in metAgenomes

virfinder

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

zenodoreadme

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