PAUDA

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_{{#uppercase: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).