N. Ahmed
20 records found
1
Authored
Comparison of Cloud-to-Cloud Distance Calculation Methods
Is the Most Complex Always the Most Suitable?
SALoBa
Maximizing Data Locality and Workload Balance for Fast Sequence Alignment on GPUs
Background: Immense improvements in sequencing technologies enable producing large amounts of high throughput and cost effective next-generation sequencing (NGS) data. This data needs to be processed efficiently for further downstream analyses. Computing systems need this larg ...
ArrowSAM
In-Memory Genomics Data Processing Using Apache Arrow
The rapidly growing size of genomics data bases, driven by advances in sequencing technologies, demands fast and cost-effective processing. However, processing this data creates many challenges, particularly in selecting appropriate algorithms and computing platforms. Computin ...
BACKGROUND: In Overlap-Layout-Consensus (OLC) based de novo assembly, all reads must be compared with every other read to find overlaps. This makes the process rather slow and limits the practicality of using de novo assembly methods at a large scale in the field. Darwin is a ...
Convolutional Neural Networks (CNNs) are a class of widely used deep artificial neural networks. However, training large CNNs to produce state-of-the-art results can take a long time. In addition, we need to reduce compute time of the inference stage for trained networks to ma ...
SparkGA2
Production-quality memory-efficient Apache Spark based genome analysis framework
Due to the rapid decrease in the cost of NGS (Next Generation Sequencing), interest has increased in using data generated from NGS to diagnose genetic diseases. However, the data generated by NGS technology is usually in the order of hundreds of gigabytes per experiment, thus ...
GASAL2
A GPU accelerated sequence alignment library for high-throughput NGS data
BACKGROUND: Due the computational complexity of sequence alignment algorithms, various accelerated solutions have been proposed to speedup this analysis. NVBIO is the only available GPU library that accelerates sequence alignment of high-throughput NGS data, but has limited pe ...
Correction to
GASAL2: A GPU accelerated sequence alignment library for high-Throughput NGS data (BMC Bioinformatics (2019) 20 (520) DOI: 10.1186/s12859-019-3086-9)
Following publication of the original article [1], the author requested changes to the figures 4, 7, 8, 9, 12 and 14 to align these with the text. The corrected figures are supplied below. The original article [1] has been corrected. [Typesetter, please insert new supplied fig ...
in analyzing such data is to map those sequenced r ...