ArticlePeerJ2020
URMAP, an ultra-fast read mapper.
Article in PeerJ, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- SARS-CoV-2 intra-host viral diversity associated with host innate and vaccine-induced immunity in an obese mouse model.BMC infectious diseases · 2026Article
- bronko: ultrafast, alignment-free detection of viral genome variation.bioRxiv : the preprint server for biology · 2026Article
- Infectome analysis of small mammals in Southern China reveals pathogen ecology and emerging risks.Nature communications · 2025Article
- Metagenomic analysis of individual mosquito viromes reveals the geographical patterns and drivers of viral diversity.Nature ecology & evolution · 2024Article
- Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation.Microbiome · 2024Article
- nail: software for high-speed, high-sensitivity protein sequence annotation.bioRxiv : the preprint server for biology · 2024Article
- Efficient mapping of accurate long reads in minimizer space with mapquik.Genome research · 2023Article
- COVID-19 mRNA vaccine protects against SARS-CoV-2 Omicron BA.1 infection in diet-induced obese mice through boosting host innate antiviral responses.EBioMedicine · 2023Article
- Strobealign: flexible seed size enables ultra-fast and accurate read alignment.Genome biology · 2022Article
- An Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes.mSphere · 2020Article
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Authors and funding
1 author.
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Abstract
Mapping of reads to reference sequences is an essential step in a wide range of biological studies. The large size of datasets generated with next-generation sequencing technologies motivates the development of fast mapping software. Here, I describe URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA with comparable accuracy on several validation tests. On a Genome in a Bottle (GIAB) variant calling test with 30× coverage 2×150 reads, URMAP achieves high accuracy (precision 0.998, sensitivity 0.982 and F-measure 0.990) with the strelka2 caller. However, GIAB reference variants are shown to be biased against repetitive regions which are difficult to map and may therefore pose an unrealistically easy challenge to read mappers and variant callers.
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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.