MedicineBow Software List

Overview

Herein, find summaries of each package with links to a more detailed page for each package.
Below is a list of software / applications that are available on MedicineBow. Click the software title to learn more about a particular software package, including its associated module name that can be used to find available versions and to load.
Please refer to our LMOD page for information about and how to use the module system:

Last Updated: 1/21/2025

application

language

C/C++	Fortran	Go
Java	Julia	Perl
Python2	Python3	R
Ruby	Rust

library

Adios2	Bison	Boost
CGAL	CGNS	Cairo
ELPA	Eigen	FFTW
GDAL	GEOS	GSL
HDF5	HYPRE	ICU4C
LAPACK	METIS	MPFR
NCURSES	NetCDF-C	NetCDF-CXX
Nettle	OpenBLAS	OpenMPI
PARMETIS	PCRE2	PETSc
Pigz	Pixman	ScaLAPACK
Scotch	Voropp	Wannier90
Zlib	Zolton

toolkit

Bedops

Cuda

SRA-Toolkit

utility

GSUtil	IOR	KentUtils
OSU Micro Benchmarks	Parallel (gnu)	RClone
qperf	stress-ng

There are 10s of utilities that will be automatically available on the System as part of the OS without needing to load a module.
Some utilities will come as part of the system but might have a module with a newer version

Astral	BWA	Bam-countread
Bcftools	Beast1	Beast2
Blast	Bowtie2	Dorado
FastQC	Fastp	Gaussian & GaussView
Guppy (CPU)	Guppy (GPU)	Hisat2
IDL	IQ-Tree	MAFFT
MATLAB	MultiQC	Muscle
Nextflow	ParaView	Picard
Qiime2	RSeQC	RegTools
SPAdes	Samtools	Subread
TopHat	Trimmomatic