The STREAM benchmark is a simple synthetic benchmark program that
measures sustainable memory bandwidth (in MB/s) and the corresponding
computation rate for simple vector kernels.
Documentation can be found at: http://www.cs.virginia.edu/stream/ref.html
Super Smack is a benchmarking, stress testing, and load generation tool
for MySQL (and PostgreSQL). Super Smack was originally written by Sasha
Pachev, and then hosted and maintained by Jeremy Zawodny.
BCFtools is a set of utilities that manipulate variant calls in the
Variant Call Format (VCF) and its binary counterpart BCF. All
commands work transparently with both VCFs and BCFs, both
uncompressed and BGZF-compressed.
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
reads per hour.
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
reads per hour.
Chemeq is a basic standalone filter written in C++ language, flex and bison.
It takes strings like: 2H2 + O2 ---> 2 H2O and can output pretty LaTeX code,
useful messages and much more. It aims to be embeddable in education tools.
gff2ps is a script program developed with the aim of converting
gff-formatted records into high quality one-dimensional plots in
PostScript. Such plots maybe useful for comparing genomic structures
and to visualizing outputs from genome annotation programs.
MUMmer is a modular system for the rapid whole genome alignment of finished
or draft sequence. This package provides an efficient suffix tree library,
seed-and-extend alignment, SNP detection, repeat detection, and
visualization tools.
HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
data. It is the core library used by samtools and bcftools.
Migrate estimates effective population sizes and past migration rates between
two or "n" populations assuming a migration matrix model with asymmetric
migration rates and different subpopulation sizes. The n-population migrate
can use sequence data, microsatellite data or electrophoretic data.