ArticleBMC bioinformatics2013
Benchmarking short sequence mapping tools.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
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Who cites it
87 citing papers in PubMed.
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- Somatic CNV Detection by Single-Cell Whole-Genome Sequencing in Postmortem Human Brain.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Evaluation of an optimized germline exomes pipeline using BWA-MEM2 and Dragen-GATK tools.PloS one · 2023Article
- Rapid genome sequencing for pediatrics.Human mutation · 2022Review
- Comparative Transcriptomic Analysis of Root and Leaf Transcript Profiles Reveals the Coordinated Mechanisms in Response to Salinity Stress in Common Vetch.International journal of molecular sciences · 2022Article
- Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software.Genome biology · 2022Article
- Assessing reproducibility of inherited variants detected with short-read whole genome sequencing.Genome biology · 2022Article
- Technology dictates algorithms: recent developments in read alignment.Genome biology · 2021Review
- Estimating sequencing error rates using families.BioData mining · 2021Article
- Dealing with Pseudogenes in Molecular Diagnostics in the Next Generation Sequencing Era.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Detailed evaluation of cancer sequencing pipelines in different microenvironments and heterogeneity levels.Turkish journal of biology = Turk biyoloji dergisi · 2021Article
- Vaccine targeting SIVmac251 protease cleavage sites protects macaques against vaginal infection.The Journal of clinical investigation · 2020Article
27 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
backgroundThe development of next-generation sequencing instruments has led to the generation of millions of short sequences in a single run. The process of aligning these reads to a reference genome is time consuming and demands the development of fast and accurate alignment tools. However, the current proposed tools make different compromises between the accuracy and the speed of mapping. Moreover, many important aspects are overlooked while comparing the performance of a newly developed tool to the state of the art. Therefore, there is a need for an objective evaluation method that covers all the aspects. In this work, we introduce a benchmarking suite to extensively analyze sequencing tools with respect to various aspects and provide an objective comparison.
resultsWe applied our benchmarking tests on 9 well known mapping tools, namely, Bowtie, Bowtie2, BWA, SOAP2, MAQ, RMAP, GSNAP, Novoalign, and mrsFAST (mrFAST) using synthetic data and real RNA-Seq data. MAQ and RMAP are based on building hash tables for the reads, whereas the remaining tools are based on indexing the reference genome. The benchmarking tests reveal the strengths and weaknesses of each tool. The results show that no single tool outperforms all others in all metrics. However, Bowtie maintained the best throughput for most of the tests while BWA performed better for longer read lengths. The benchmarking tests are not restricted to the mentioned tools and can be further applied to others.
conclusionThe mapping process is still a hard problem that is affected by many factors. In this work, we provided a benchmarking suite that reveals and evaluates the different factors affecting the mapping process. Still, there is no tool that outperforms all of the others in all the tests. Therefore, the end user should clearly specify his needs in order to choose the tool that provides the best results.
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Registered trials
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.