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SAMZIP | Improving transmission efficiency of large sequence alignment/map (SAM) files

Allows to encode Sequence Alignment/Map (SAM) files. SAMZIP is an encoding scheme specifically designed to work on SAM files. The scheme exploits two important characteristic of SAM files to improve compression ratio, and consequently the transmission time.

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SAMZIP classification

SAMZIP specifications

Unique identifier:
Command line interface
Operating system:
Computer skills:
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Programming languages:

SAMZIP distribution


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SAMZIP support


  • Chin-Tser Huang <>


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Department of Computer Science & Engineering, University of South Carolina, Columbia, SC, USA; Department of Biochemistry, Medical University of South Carolina, Charleston, SC, USA

Funding source(s)

Partially supported by National Science Foundation (NSF) under the grant NSF CNS 0916857, National Science Foundation (NSF) under the grant NSF OCI 0904179, 1UL RR029882-01, NIH/NIGMS R01GM063265-09S1 and a pilot project from grant NIH/NCRR P20 RR017677 and PhRMA Foundation Research Starter Grant.

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