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microbiome_helper

An assortment of scripts to help process and automate various microbiome and metagenomic bioinformatic tools.

microfiltr

accessory functions for processing microbial community data

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

ministat

A small tool to do the statistics legwork on benchmarks etc.

mlst

Scan contig files against PubMLST typing schemes

mothur

Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Immunology at The University of Michigan. This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

musicc

MUSiCC: A marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome

mykrobe-predictor

Antibiotic resistance predictions in minutes on a laptop

nanopore

Software for nanopore data analysis

nanopore_urine_analysis

nanostripper

Strip reads from Oxford Nanopore FAST5 files if they meet certain criteria

nasp

Northern Arizona SNP Pipeline

ncov-watch

Tools for detecting mutations of interest in SARS-CoV-2 sequencing results

nextflow

A DSL for data-driven computational pipelines

nextflow-examples

A collection of examples introducing to Nextflow scripting

nullarbor

Pipeline to generate complete public health microbiology reports from Illumnina sequenced isolates

oneliners

Useful bash one-liners for bioinformatics.

orthomcl-pipeline

Automates running of OrthoMCL software from http://orthomcl.org/common/downloads/software/v2.0/

pan-genome-analysis

Processing pipeline for pan-genome visulization and exploration

pandemix

panseq

Pan-genomic sequence analysis

pavian

🌈 Interactive analysis of metagenomics data

phastaf

Identify phage regions in bacterial genomes for masking purposes

phigaro

Phigaro is a scalable command-line tool for predictions phages and prophages from nucleid acid sequences (including metagenomes) and is based on phage genes HMMs and a smoothing window algorithm.

pileup.js

Interactive in-browser track viewer

pilon

Pilon is an automated genome assembly improvement and variant detection tool

pipelines

BASH scripted pipelines for accurate de novo assembly, variant calling, and validation in and for parasite genomes

plasmid_comp

plasmidprofiler-galaxy