Jan 21, 2013 · The mapper follows six steps to map a query read to the reference genome. In step 1, the mapper divides the query read into smaller k-mers, with ...

Figure 1: The flow chart of hash table based mappers. 1) Divide the input read into smaller k-mers. 2). Search each k-mer in the hash table previously ...

We propose a new algorithm, FastHASH, which drastically improves the performance of the seed-and-extend type hash table based read mapping algorithms, while ...

Accelerating Read Mapping with FastHASH. Hongyi Xin† Donghyuk Lee† Farhad ... http://www.ece.cmu.edu/~safari. 31. Accelerating Read Mapping with FastHASH.

With the introduction of next-generation sequencing (NGS) technologies, we are facing an exponential increase in the amount of genomic sequence data.

Jan 20, 2013 · We propose a new algorithm, FastHASH, which drastically improves the performance of the seed-and-extend type hash table based read mapping ...

Accelerating read mapping with FastHASH. H Xin, D Lee, F Hormozdiari, S ... Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate ...

Jun 21, 2023 · One of the most computationally demanding steps in analyzing sequencing data is mapping short reads produced by NGS to a reference DNA sequence, ...

The goal of this project is to develop specialized hardware architectures to accelerate mapping reads generated with the high throughput sequencing platforms.