Huxelerate Ready to use services

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Library

Function FPGA GPU
Sequence Aligner
Signal Aligner
ksw2c Aligner
ksw2s Aligner

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Applications

Application FPGA GPU
Hugenomic Nanopolish

Free Trial on AWS and Huxelerate Platform

Want to see you open/closed source application here? Let's talk!

Library Description

Sequence Aligner

Huxelerate sequence aligner computes a similarity measure of two text sequences or subsequences and identifies the best way to align them according to a user-defined scoring scheme. The function perform an accelerated version of Smith-Waterman and Needleman–Wunsch alignment algorithms, computational bottlenecks in bioinformatic which find applications also in computer security and text analysis.

Signal Aligner

Huxelerate signal aligner computes a similarity measure across two time series which may vary in speed. The function implements an accelerated version of the Dynamic Time Warping algorithm, a computational bottleneck for signal classification and recognition tasks. Example applications involve genome sequencing and analysis with nanopore technology, connected health with ECG-based diagnostic and humanized machines with speech recognition.

Ksw2c Aligner

Huxelerate ksw2c aligner computes the optimal scores and the CIGAR for global and extension alignment of two sequences using dual gap affine cost function and a custom scoring matrix. The core also supports banded alignment and the z-drop heuristics - info here The function implements an accelerated version of ksw2_extd software

ksw2s Aligner

Huxelerate ksw2s provides the same functionality as ksw2c aligner but the CIGAR. This FPGA implementation is in fact optimized in performance to calculate only the optimal scores.

Applications Description

Hugenomic Nanopolish

Huxelerate Hugenomic Nanopolish enables ultra-fast signal-level analysis of large datasets of Oxford Nanopore Sequencing data. The software is based on Nanopolish and can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more. Current release allows to accelerate the eventalign tool, reducing computational time from days to hours when compared to software-only executions on AWS.