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Found 13 papers, 5 papers with code
MetaTrinity: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation
This dual comparison positions MetaTrinity as a broadly applicable solution for metagenomic classification, combining advantages of both ends of the spectrum: speed and accuracy.
SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences
Comparing genomic sequences is one of the most fundamental computational steps in most genomic analyses.
A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater
Here, we perform comprehensive benchmarking of 18 bioinformatics methods for estimating the relative abundance of SARS-CoV-2 (sub)lineages in wastewater by using data from 36 in vitro mixtures of synthetic lineage and sublineage genomes.
SARS-CoV-2 Wastewater Genomic Surveillance: Approaches, Challenges, and Opportunities
The existing bioinformatics tools used to analyze wastewater sequencing data are often based on previously developed methods for quantifying the expression of transcripts or viral diversity.
Genomic reproducibility in the bioinformatics era
In biomedical research, validation of a new scientific discovery is tied to the reproducibility of its experimental results.
Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities
Omics software tools have reshaped the landscape of modern biology and become an essential component of biomedical research.
Unlocking capacities of viral genomics for the COVID-19 pandemic response
More than any other infectious disease epidemic, the COVID-19 pandemic has been characterized by the generation of large volumes of viral genomic data at an incredible pace due to recent advances in high-throughput sequencing technologies, the rapid global spread of SARS-CoV-2, and its persistent threat to public health.
Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure
While this viral species was unknown prior to January 2020, its similarity to other coronaviruses that infect humans has allowed for rapid insight into the mechanisms that it uses to infect human hosts, as well as the ways in which the human immune system can respond.
Diversity in immunogenomics: the value and the challenge
With the advent of high-throughput sequencing technologies, the fields of immunogenomics and adaptive immune receptor repertoire research are facing both opportunities and challenges.
RNA-seq data science: From raw data to effective interpretation
RNA-seq is a method of analyzing the RNA content of a sample using the modern sequencing platforms.
Technology dictates algorithms: Recent developments in read alignment
We separately discuss how longer read lengths produce unique advantages and limitations to read alignment techniques.
Recommendations to enhance rigor and reproducibility in biomedical research
Computational methods have reshaped the landscape of modern biology.
Metagenomics for clinical diagnostics: technologies and informatics
The human-associated microbiome is closely tied to human health and is of substantial clinical interest.
