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: 11/12/24

application

language

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

library

Adios2	Bison	Boost
Cairo	CGAL	CGNS
Cuda	Eigen	ELPA
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

We haves 10s of libraries and do not have a wiki page for them all. We recommend, once you have access, to perform a module spider to see if it is installed, but not listed above.

toolkit

Bedops

Cuda

SRA-Toolkit

utility

GSUtil	IOR	KentUtils
OSU Micro Benchmarks	Parallel (gnu)	qperf
RClone	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	Bam-countread	Bcftools
Beast1	Beast2	Blast
Bowtie2	Dorado	Fastp
FastQC	Gaussian & GaussView	Guppy (CPU)
Guppy (GPU)	Hisat2	IDL
IQ-Tree	MAFFT	MATLAB
MultiQC	Muscle	Nextflow
ParaView	Picard	Qiime2
RegTools	RSeQC	Samtools
SPAdes	Subread	TopHat
Trimmomatic