Article

Easing genomic surveillance: A comprehensive performance evaluation of long-read assemblers across multi-strain mixture data of HIV-1 and Other pathogenic viruses for constructing a user-friendly bioinformatic pipeline

2024-05-31

Abstract excerpt

Background Determining the appropriate computational requirements and software performance is essential for efficient genomic surveillance. The lack of standardized benchmarking complicates software selection, especially with limited resources. Methods We developed a containerized benchmarking pipeline to evaluate seven long-read assemblers—Canu, GoldRush, MetaFlye, Strainline, HaploDMF, iGDA, and RVHaplo—for vira...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: 4152c3d2-fcd4-5f73-94c8-320498d29d37
DOI: 10.12688/f1000research.149577.1

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Easing genomic surveillance: A comprehensive performance evaluation of long-read assemblers across multi-strain mixture data of HIV-1 and Other pathogenic viruses for constructing a user-friendly bioinformatic pipelineDOI 10.12688/f1000research.149577.1Read

Evaluating assembly and variant calling software for strain-resolved analysis of large DNA-virusesSemantic proximity Read

Comparative Evaluation of Bioinformatic Pipelines for Full-Length Viral Genome AssemblySemantic proximity Read

Evaluating assembly and variant calling software for strain-resolved analysis of large DNA viruses.Semantic proximity Read

Complementary insights into gut viral genomes: a comparative benchmark of short- and long-Read metagenomes using diverse assemblers and binnersSemantic proximity Read

Strainline: full-length de novo viral haplotype reconstruction from noisy long readsSemantic proximity Read

Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic WorkflowsSemantic proximity Read

Enhancing public health surveillance: a comparative study of platform-specific and hybrid assembly approaches in SARS-CoV-2 genome sequencing.Semantic proximity Read

Comparison and benchmark of gut viral genomes detected from short- and long-read metagenomesSemantic proximity Read

MALVIRUS: an integrated application for viral variant analysis.Semantic proximity Read

VirAmp: a galaxy-based viral genome assembly pipelineSemantic proximity Read

VirGenA: a reference-based assembler for variable viral genomes.Semantic proximity Read

SNVPhyl: A Single Nucleotide Variant Phylogenomics pipeline for microbial genomic epidemiologySemantic proximity Read