Related papers: RECKONER: Read Error Corrector Based on KMC
Large-scale genomic workflows used in precision medicine can process datasets spanning tens to hundreds of gigabytes per sample, leading to high memory spikes, intensive disk I/O, and task failures due to out-of-memory errors. Simple static…
Motivation: Next generation methods of DNA sequencing produce relatively high rate of reading errors, which interfere with de novo genome assembly of newly sequenced organisms and particularly affect the quality of SNP detection important…
Genomics is the critical key to enabling precision medicine, ensuring global food security and enforcing wildlife conservation. The massive genomic data produced by various genome sequencing technologies presents a significant challenge for…
As quantum computing moves toward fault-tolerant architectures, quantum error correction (QEC) decoder performance is increasingly critical for scalability. Understanding the impact of transitioning from floating-point software to…
Quantum error correction codes (QECC) are a key component for realizing the potential of quantum computing. QECC, as its classical counterpart (ECC), enables the reduction of error rates, by distributing quantum logical information across…
Automated compilation error repair, the problem of suggesting fixes to buggy programs that fail to compile, has generated significant interest in recent years. Apart from being a tool of general convenience, automated code repair has…
Read mapping is a fundamental, yet computationally-expensive step in many genomics applications. It is used to identify potential matches and differences between fragments (called reads) of a sequenced genome and an already known genome…
Quantum error-correcting codes (QECCs) can eliminate the negative effects of quantum noise, the major obstacle to the execution of quantum algorithms. However, realizing practical quantum error correction (QEC) requires resolving many…
The emergence of Next Generation Sequencing (NGS) platforms has increased the throughput of genomic sequencing and in turn the amount of data that needs to be processed, requiring highly efficient computation for its analysis. In this…
Nanopore sequencing can read substantially longer sequences of nucleic acid molecules, called reads, than other sequencing methods, which has led to advances in genomic analysis such as the gapless human genome assembly. By analyzing the…
Motivation: Despite significant advances in Third-Generation Sequencing (TGS) technologies, Next-Generation Sequencing (NGS) technologies remain dominant in the current sequencing market. This is due to the lower error rates and richer…
New long read sequencing technologies, like PacBio SMRT and Oxford NanoPore, can produce sequencing reads up to 50,000 bp long but with an error rate of at least 15%. Reducing the error rate is necessary for subsequent utilisation of the…
Reconciliation is a crucial procedure in post-processing of Quantum Key Distribution (QKD), which is used for correcting the error bits in sifted key strings. Although most studies about reconciliation of QKD focus on how to improve the…
Optimizing deep learning models is generally performed in two steps: (i) high-level graph optimizations such as kernel fusion and (ii) low level kernel optimizations such as those found in vendor libraries. This approach often leaves…
Nanopore sequencing, superior to other sequencing technologies for DNA storage in multiple aspects, has recently attracted considerable attention. Its high error rates, however, demand thorough research on practical and efficient coding…
Quantum error correction is widely thought to be the key to fault-tolerant quantum computation. However, determining the most suited encoding for unknown error channels or specific laboratory setups is highly challenging. Here, we present a…
Quantum error correction (QEC) will be essential to achieve the accuracy needed for quantum computers to realise their full potential. The field has seen promising progress with demonstrations of early QEC and real-time decoded experiments.…
Quantum computers have the possibility of a much reduced calculation load compared with classical computers in specific problems. Quantum error correction (QEC) is vital for handling qubits, which are vulnerable to external noise. In QEC,…
Aligning millions of short DNA or RNA reads, of 75 to 250 base pairs each, to a reference genome is a significant computation problem in bioinformatics. We present a flexible and fast FPGA-based short read alignment tool. Our aligner makes…
Due to the low error tolerance of a qubit, detecting and correcting errors on it is essential for fault-tolerant quantum computing. Surface code (SC) associated with its decoding algorithm is one of the most promising quantum error…