Related papers: MetaStore: High-Performance Metagenomic Analysis v…
Metagenomics has led to significant advances in many fields. Metagenomic analysis commonly involves the key tasks of determining the species present in a sample and their relative abundances. These tasks require searching large metagenomic…
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…
Metagenomics, the study of genome sequences of diverse organisms cohabiting in a shared environment, has experienced significant advancements across various medical and biological fields. Metagenomic analysis is crucial, for instance, in…
Metagenomics is an emerging field of molecular biology concerned with analyzing the genomes of environmental samples comprising many different diverse organisms. Given the nature of metagenomic data, one usually has to sequence the genomic…
Up-to-date meta-databases are vital for the analysis of biological data. However,the current exponential increase in biological data leads to exponentially increasing meta-database sizes. Large-scale meta-database management is therefore an…
Metagenomics offers a way to analyze biotopes at the genomic level and to reach functional and taxonomical conclusions. The bio-analyzes of large metagenomic projects face critical limitations: complex metagenomes cannot be assembled and…
The cost of DNA sequencing has dropped exponentially over the past decade, making genomic data accessible to a growing number of scientists. In bioinformatics, localization of short DNA sequences (reads) within large genomic sequences is…
Data distribution across different facilities offers benefits such as enhanced resource utilization, increased resilience through replication, and improved performance by processing data near its source. However, managing such data is…
We introduce a parallel algorithmic architecture for metagenomic sequence assembly, termed MetaPar, which allows for significant reductions in assembly time and consequently enables the processing of large genomic datasets on computers with…
Minimizing data storage poses a significant challenge in large-scale metagenomic projects. In this paper, we present a new method for improving the encoding of FASTQ files generated by metagenomic sequencing. This method incorporates…
In large-scale distributed file systems, efficient meta- data operations are critical since most file operations have to interact with metadata servers first. In existing distributed hash table (DHT) based metadata management systems, the…
Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is…
This study proposes a novel storage engine, SynchroStore, designed to address the inefficiency of update operations in columnar storage systems based on Log-Structured Merge Trees (LSM-Trees) under hybrid workload scenarios. While columnar…
MetaScope is a fast and accurate tool for analyzing (host-associated) metagenome datasets. Sequence alignment of reads against the host genome (if requested) and against microbial Genbank is performed using a new DNA aligner called SASS.…
The rise of microservice architectures has revolutionized application design, fostering adaptability and resilience. These architectures facilitate scaling and encourage collaborative efforts among specialized teams, streamlining deployment…
Metagenomic profiling is challenging in part because of the highly uneven sampling of the tree of life by genome sequencing projects and the limitations imposed by performing phylogenetic inference at fixed taxonomic ranks. We present the…
Metagenomic studies have increasingly utilized sequencing technologies in order to analyze DNA fragments found in environmental samples.One important step in this analysis is the taxonomic classification of the DNA fragments. Conventional…
Many previous works in spike sorting study spike classification and compression independently. In this paper, a novel algorithm is proposed called MetaSort to address these two problems. To deal with compression, a novel adaptive level…
This paper introduces the first open-source FPGA-based infrastructure, MetaSys, with a prototype in a RISC-V core, to enable the rapid implementation and evaluation of a wide range of cross-layer techniques in real hardware.…
Motivation: Accurate data analysis and quality control is critical for metagenomic studies. Though many tools exist to analyze metagenomic data there is no consistent framework to integrate and run these tools across projects. Currently,…