With the recent move towards sequencing of accurate long reads, finding
solutions that support efficient analysis of these reads becomes more
necessary. The long execution time required for sequence alignment of long
reads negatively affects genomic studies relying on sequence alignment.
Although pre-alignment filtering as an extra step before alignment was recently
introduced to mitigate sequence alignment for short reads, these filters do not
work as efficiently for long reads. Moreover, even with efficient pre-alignment
filters, the overall end-to-end (i.e., filtering + original alignment)
execution time of alignment for long reads remains high, while the filtering
step is now a major portion of the end-to-end execution time.
Our paper makes three contributions. First, it identifies data movement of
sequences between memory units and computing units as the main source of
inefficiency for pre-alignment filters of long reads. This is because although
filters reject many of these long sequencing pairs before they get to the
alignment stage, they still require a huge cost regarding time and energy
consumption for the large data transferred between memory and processor.
Second, this paper introduces an adaptation of a short-read pre-alignment
filtering algorithm suitable for long reads. We call this LongGeneGuardian.
Finally, it presents Filter-Fuse as an architecture that supports
LongGeneGuardian inside the memory. FilterFuse exploits the
Computation-In-Memory computing paradigm, eliminating the cost of data movement
in LongGeneGuardian.
Our evaluations show that FilterFuse improves the execution time of filtering
by 120.47x for long reads compared to State-of-the-Art (SoTA) filter,
SneakySnake. FilterFuse also improves the end-to-end execution time of sequence
alignment by up to 49.14x and 5207.63x compared to SneakySnake with SoTA
aligner and only SoTA aligner, respectively