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PASHA

Takes advantage of hybrid computing architectures consisting of both shared-memory multi-core CPUs and distributed-memory compute clusters to gain efficiency and scalability. PASHA is a parallelized short read assembler using de Bruijn graphs (DBG) that is able to produce more contiguous high-quality assemblies in shorter time compared to three leading assemblers: Velvet, ABySS and SOAPdenovo. It employs a sorted vector data structure, instead of a hash-map, to store k-mers and their graph-related information.

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PASHA forum

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PASHA classification

PASHA specifications

Software type:
Package/Module
Restrictions to use:
None
Computer skills:
Advanced
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux
Stability:
Stable

PASHA distribution

versioning

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No versioning.

PASHA support

Documentation

Maintainer

  • Yongchao Liu <>

Credits

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Publications

Institution(s)

School of Computer Engineering, Nanyang Technological University, Singapore; Institut für Informatik, Johannes Gutenberg University Mainz, Germany

Link to literature

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