Purdue University

Medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data.

Meep or MEEP is a free finite-difference time-domain FDTD simulation software package developed at MIT to model electromagnetic systems.

Megadepth is an efficient tool for extracting coverage related information from RNA and DNA-seq BAM and BigWig files.

Megahit is a ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.

Megan is a computer program that allows optimized analysis of large metagenomic datasets. Metagenomics is the analysis of the genomic sequences from a usually uncultured environmental sample.

Meme is a collection of tools for the discovery and analysis of sequence motifs.

memes is an R interface to the MEME Suite family of tools, which provides several utilities for performing motif analysis on DNA, RNA, and protein sequences. memes works by detecting a local install of the MEME suite, running the commands, then importing the results directly into R.

Meraculous is a whole genome assembler for Next Generation Sequencing data, geared for large genomes. It is hybrid k-mer/read-based approach capitalizes on the high accuracy of Illumina sequence by eschewing an explicit error correction step which we argue to be redundant with the assembly process.

Merqury is a tool to evaluate genome assemblies with k-mers and more.

Meryl is a genomic k-mer counter (and sequence utility) with nice features.

This package provides the Mesa OpenGL Utility library.

Metabat is a robust statistical framework for reconstructing genomes from metagenomic data.

Metachip is a pipeline for Horizontal gene transfer (HGT) identification.

MetaHipMer is a de novo metagenome short-read assembler. Version 2 (MHM2) is written entirely in UPC++ and runs efficiently on both single servers and on multinode supercomputers, where it can scale up to coassemble terabase-sized metagenomes.

MetaPhlAn (Metagenomic Phylogenetic Analysis) is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.

Metaseq is a Python package for integrative genome-wide analysis reveals relationships between chromatin insulators and associated nuclear mRNA.

MethylDackel (formerly named PileOMeth, which was a temporary name derived due to it using a PILEup to extract METHylation metrics) will process a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments and extract per-base methylation metrics from them. MethylDackel requires an indexed fasta file containing the reference genome as well.

Metilene is a versatile tool to study the effect of epigenetic modifications in differentiation/development, tumorigenesis, and systems biology on a global, genome-wide level.

MicrobeDMM is a suite of programs used for empirical Bayes fitting of DMM models.

The Microsoft Cognitive Toolkit is a unified deep-learning toolkit that describes neural networks as a series of computational steps via a directed graph.