ArticleBioinformatics (Oxford, England)2013
GAGE-B: an evaluation of genome assemblers for bacterial organisms.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
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Who cites it
74 citing papers in PubMed.
- Hidden Markov Model-Based Prokaryotic Genome Space Mining Reveals the Widespread Pervasiveness of Complex I and Its Potential Evolutionary Scheme.Genome biology and evolution · 2025Article
- An overlooked phenomenon: complex interactions of potential error sources on the quality of bacterial de novo genome assemblies.BMC genomics · 2024Article
- Benchmarking State-of-the-Art Approaches for Norovirus Genome Assembly in Metagenome Sample.Biology · 2023Article
- WebQUAST: online evaluation of genome assemblies.Nucleic acids research · 2023Article
- A practical comparison of the next-generation sequencing platform and assemblers using yeast genome.Life science alliance · 2023Article
- metaMIC: reference-free misassembly identification and correction of de novo metagenomic assemblies.Genome biology · 2022Article
- Software Choice and Sequencing Coverage Can Impact Plastid Genome Assembly-A Case Study in the Narrow EndemicFrontiers in plant science · 2022Article
- EvalDNA: a machine learning-based tool for the comprehensive evaluation of mammalian genome assembly quality.BMC bioinformatics · 2021Article
- Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences.PLoS biology · 2021Article
- Antimicrobial susceptibilities and comparative whole genome analysis of two isolates of the probiotic bacterium Lactiplantibacillus plantarum, strain ATCC 202195.Scientific reports · 2021Article
- Combination of mass spectrometry and DNA sequencing for detection of antibiotic resistance in diagnostic laboratories.Folia microbiologica · 2020Review
- Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data.Briefings in bioinformatics · 2019Article
- SQUAT: a Sequencing Quality Assessment Tool for data quality assessments of genome assemblies.BMC genomics · 2019Article
- GMASS: a novel measure for genome assembly structural similarity.BMC bioinformatics · 2019Article
- MAC: Merging Assemblies by Using Adjacency Algebraic Model and Classification.Frontiers in genetics · 2019Article
- Assessing the impact of exact reads on reducing the error rate of read mapping.BMC bioinformatics · 2018Article
- Versatile genome assembly evaluation with QUAST-LG.Bioinformatics (Oxford, England) · 2018Article
- Bioinformatic Workflows for Generating Complete Plastid Genome Sequences-An Example fromLife (Basel, Switzerland) · 2018Article
- riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions.Nucleic acids research · 2018Article
- Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains.BMC genomics · 2018Article
14 more citing papers are in PubMed but not listed here.
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8 authors.
Funding
Abstract
motivationA large and rapidly growing number of bacterial organisms have been sequenced by the newest sequencing technologies. Cheaper and faster sequencing technologies make it easy to generate very high coverage of bacterial genomes, but these advances mean that DNA preparation costs can exceed the cost of sequencing for small genomes. The need to contain costs often results in the creation of only a single sequencing library, which in turn introduces new challenges for genome assembly methods.
resultsWe evaluated the ability of multiple genome assembly programs to assemble bacterial genomes from a single, deep-coverage library. For our comparison, we chose bacterial species spanning a wide range of GC content and measured the contiguity and accuracy of the resulting assemblies. We compared the assemblies produced by this very high-coverage, one-library strategy to the best assemblies created by two-library sequencing, and we found that remarkably good bacterial assemblies are possible with just one library. We also measured the effect of read length and depth of coverage on assembly quality and determined the values that provide the best results with current algorithms. CONTACT: salzberg@jhu.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.