This is the Linux app named PASHA: Parallelized Short Read Assembly whose latest release can be downloaded as Pasha-1.0.10.tar.bz2. It can be run online in the free hosting provider OnWorks for workstations.
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PASHA: Parallelized Short Read Assembly
DESCRIPTION:
PASHA is a parallel short read assembler for large genomes using de Bruijn graphs. Taking advantage of both shared-memory multi-core CPUs and distributed-memory compute clusters, PASHA has demonstrated its potential to perform high-quality de-novo assembly of large genomes in reasonable time with modest computing resources. Our evaluation using three small real paired-end datasets shows that PASHA is able to produce better assemblies with comparable genome coverage and mis-assembly rates compared to three leading assemblers: Velvet, ABySS and SOAPdenovo. Moreover, PASHA achieves the fastest speed for all three datasets on a single CPU. For the human genome, PASHA achieves competitive assembly quality with ABySS and is able to complete the assembly in about 21 hours, which is about 2.38× faster than ABySS on the same hardware configurations.
User interface
Console/Terminal
Programming Language
C++
Categories
This is an application that can also be fetched from https://sourceforge.net/projects/pasha/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.