ArticleBMC genomics2019
Exploring the unmapped DNA and RNA reads in a songbird genome.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Chromosome-level genome assembly of the sand martin (Riparia riparia).Scientific data · 2026Article
- SwarmGenomics: A Unified Pipeline for Individual-Based Whole-Genome Analyses.Molecular ecology resources · 2026Article
- Isolation and characterization of a novel lytic bacteriophage Ecolivirus Myo-P293 targeting avian pathogenic Escherichia coli.Archives of virology · 2026Article
- Decoding the Avian Missing Gene Mystery: Dot Chromosomes Unmask Extensive Gene Loss and Novel Genetic Instability.Genome biology and evolution · 2026Article
- Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes.Genome research · 2025Article
- Advantages of Mutant Generation by Genome Rearrangements of Non-Conventional Yeast via Direct Nuclease Transfection.Genes to cells : devoted to molecular & cellular mechanisms · 2025Article
- Faecal metagenomes of great tits and blue tits provide insights into host, diet, pathogens and microbial biodiversity.Access microbiology · 2025Article
- The effect of missing data on evolutionary analysis of sequence capture bycatch, with application to an agricultural pest.Molecular genetics and genomics : MGG · 2024Article
- Transcriptional and functional predictors of potato virus Y-induced tuber necrosis in potato (Frontiers in plant science · 2024Article
- Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in german black Pied cattle.Veterinary research · 2023Article
- Article
- Another lesson from unmapped reads: in-depth analysis of RNA-Seq reads from various horse tissues.Journal of applied genetics · 2022Article
- The human "contaminome": bacterial, viral, and computational contamination in whole genome sequences from 1000 families.Scientific reports · 2022Article
- Article
- Sequencing refractory regions in bird genomes are hotspots for accelerated protein evolution.BMC ecology and evolution · 2021Article
- Adaptive markers distinguish North and South Pacific Albacore amid low population differentiation.Evolutionary applications · 2021Article
- Humic-acid-driven escape from eye parasites revealed by RNA-seq and target-specific metabarcoding.Parasites & vectors · 2020Article
- Comparative RNA-Seq transcriptome analyses reveal dynamic time-dependent effects ofBMC genomics · 2020Article
- CAFU: a Galaxy framework for exploring unmapped RNA-Seq data.Briefings in bioinformatics · 2020Article
- Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
backgroundA widely used approach in next-generation sequencing projects is the alignment of reads to a reference genome. Despite methodological and hardware improvements which have enhanced the efficiency and accuracy of alignments, a significant percentage of reads frequently remain unmapped. Usually, unmapped reads are discarded from the analysis process, but significant biological information and insights can be uncovered from these data. We explored the unmapped DNA (normal and bisulfite treated) and RNA sequence reads of the great tit (Parus major) reference genome individual. From the unmapped reads we generated de novo assemblies, after which the generated sequence contigs were aligned to the NCBI non-redundant nucleotide database using BLAST, identifying the closest known matching sequence.
resultsMany of the aligned contigs showed sequence similarity to different bird species and genes that were absent in the great tit reference assembly. Furthermore, there were also contigs that represented known P. major pathogenic species. Most interesting were several species of blood parasites such as Plasmodium and Trypanosoma.
conclusionsOur analyses revealed that meaningful biological information can be found when further exploring unmapped reads. For instance, it is possible to discover sequences that are either absent or misassembled in the reference genome, and sequences that indicate infection or sample contamination. In this study we also propose strategies to aid the capture and interpretation of this information from unmapped reads.
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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.