PUNASfilter

We present a parallel ungapped-alignment-featured seed verification (PUNAS) algorithm, a fast filter for effectively removing the majority of false positive seeds, thus significantly accelerating the short-read alignment process. PUNAS is based on bit-parallelism and takes advantage of SIMD vector units of modern microprocessors. PUNAS algorithm expands the basic Hamming distance computation, which only detects substitutions, into a full-fledged edit-distance filter, which counts not only substitutions but insertions and deletions as well.

We have implemented our PUNAS algorithm as a standalone application (PUNASfilter) that can be incorporated into existing seed-and-extend based SRA tools. PUNASfilter is a filter that detects and filters some of the string pairs that have edit-distances that are greater than error threshold T, but it does not validate the string pairs that pass the filter regarding if they have edit-distances smaller than T. In a DNA mapper or protein mapper, PUNASfilter should then be extended by a more expensive DP-based alignment method. The PUNASfilter application is written in OpenMPaugmented C++. Our implementation employs a vectorize-and-scale approach and can be execyted on multi-core CPUs and many-core Knights Landing (KNL)-based Xeon Phi processors as well.

Currently, we presents three implementations: they are PUNAS-SSE, PUNAS-AVX2, PUNAS-AVX512. They are implemented using Intel SSE, AVX2 and AVX512 instructuon set respectively. Besides, the query string length is not limited by vector registers size. Although currently PUNAS only supports mapping DNA, it can be easily expanded to support protein matching. Please directly contact the author if you need such functionality.

Getting started

To build PUNAS, after you choose one in three implementation, based on your hardware platform, then simply

do:

$make

Running a test

To run a test using PUNAS, simply do:

$ ./PUNAS <reference file> <read file> <error threashold>

After the execution is finished, a summary of the run is printed out, including the total number of string pairs processed and the total number of string pairs pass PUNAS.