PAUDA

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Description

PAUDA website  

PAUDA is a new approach toward the problem of comparing DNA reads against a database of protein reference sequences that is applicable to very large datasets consisting of hundreds of millions or billions of reads. PAUDA is an acronym for "Protein Alignment Using a DNA Aligner". The approach allows one to harness the high efficiency of DNA read aligners to compute BLASTX-like alignments between sequencing reads and a protein database in a small fraction of the time required by BLASTX. The PAUDA approach makes it possible to process DNA reads at a rate of millions of reads per CPU hour. PAUDA is 10,000 times faster than BLASTX.

Required Modules

Serial

  • PAUDA

Parallel (OpenMP)

  • intel
  • PAUDA

Parallel (MPI)

  • intel
  • openmpi
  • PAUDA

System Variables

  • HPC_PAUDA_DIR - installation directory




Citation

If you publish research that uses PAUDA you have to cite it as follows:

Daniel H. Huson and Chao Xie, A poor man’s BLASTX - high-throughput metagenomic protein database search using PAUDA, submitted to HitSeq (2013).


Validation

  • Validate 4/5/2018