art-nextgen-simulation-tools-profiles

profiles for art simulation tools

ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms: Illumina's Solexa, Roche's 454 and Applied Biosystems' SOLiD. ART can be used to test or benchmark a variety of method or tools for next-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART was used as a primary tool for the simulation study of the 1000 Genomes Project . ART is implemented in C++ with optimized algorithms and is highly efficient in read simulation. ART outputs reads in the FASTQ format, and alignments in the ALN format. ART can also generate alignments in the SAM alignment or UCSC BED file format. ART can be used together with genome variants simulators (e.g. VarSim) for evaluating variant calling tools or methods.

quagga-ospfd

OSPF routing daemon

GNU Quagga is free software which manages TCP/IP based routing protocols. It supports BGP4, BGP4+, OSPFv2, OSPFv3, IS-IS, RIPv1, RIPv2, and RIPng as well as the IPv6 versions of these.

libgphobos76-mips64-cross

Phobos D standard library (runtime library)

This is the Phobos standard library that comes with the D2 compiler.

uhexen2

Hexen II - engine package

Hammer of Thyrion is a Hexen II engine

libio-pager-perl

module to select a pager and pipe text to it

IO::Pager is lightweight and can be used to locate an available pager and set the PAGER environment variable sanely or as a factory for creating objects defined elsewhere such as IO::Pager::Buffered, IO::Pager::Unbuffered, and IO::Pager::less which provides a pure perl pager.

pypy-setuptools

PyPy Distutils Enhancements

Extensions to the python-distutils for large or complex distributions.