ArticleBioinformatics (Oxford, England)2020
CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis.mSystems · 2026Article
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- Host albumin redirects Candida albicans metabolism to engage an alternative pathogenicity pathway.Nature communications · 2025Article
- Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC.Genome research · 2025Article
- Investigating the transcriptional fingerprints of coculturedFrontiers in microbiology · 2025Article
- Insights into the origin, hybridisation and adaptation of Candida metapsilosis hybrid pathogens.PLoS pathogens · 2025Article
- INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance.Genome medicine · 2024Article
- A multidimensional assessment of in-host fitness costs of drug resistance in the opportunistic fungal pathogen Candida glabrata.FEMS yeast research · 2024Article
- Long-term stability of acquired drug resistance and resistance associated mutations in the fungal pathogenFrontiers in cellular and infection microbiology · 2024Article
- Origin of fungal hybrids with pathogenic potential from warm seawater environments.Nature communications · 2023Article
- Reconstruction of the personal information from human genome reads in gut metagenome sequencing data.Nature microbiology · 2023Article
- Pitfalls of genotyping microbial communities with rapidly growing genome collections.Cell systems · 2023Article
- Article
- Multiplexed target enrichment of coding and non-coding transcriptomes enables studyingFrontiers in cellular and infection microbiology · 2023Article
- Narrow mutational signatures drive acquisition of multidrug resistance in the fungal pathogen Candida glabrata.Current biology : CB · 2021Article
- Candida pathogens induce protective mitochondria-associated type I interferon signalling and a damage-driven response in vaginal epithelial cells.Nature microbiology · 2021Article
- Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid for the Diagnosis of Cerebral Aspergillosis.Frontiers in microbiology · 2021Article
- Integrative Omics Analysis Reveals a Limited Transcriptional Shock After Yeast Interspecies Hybridization.Frontiers in genetics · 2020Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationNumerous sequencing studies, including transcriptomics of host-pathogen systems, sequencing of hybrid genomes, xenografts, mixed species systems, metagenomics and meta-transcriptomics, involve samples containing genetic material from divergent organisms. A crucial step in these studies is identifying from which organism each sequencing read originated, and the experimental design should be directed to minimize biases caused by cross-mapping of reads to incorrect source genomes. Additionally, pooling of sufficiently different genetic material into a single sequencing library could significantly reduce experimental costs but requires careful planning and assessment of the impact of cross-mapping. Having these applications in mind we designed Crossmapper, the first to our knowledge tool able to assess cross-mapping prior to sequencing, therefore allowing optimization of experimental design.
resultsUsing any combination of reference genomes, Crossmapper performs read simulation and back-mapping of those reads to the pool of references, quantifies and reports the cross-mapping rates for each organism. Crossmapper performs these analyses with numerous user-specified parameters, including, among others, read length, read layout, coverage, mapping parameters, genomic or transcriptomic data. Additionally, it outputs the results in highly interactive and publication-ready reports. This allows the user to perform multiple comparisons at once and choose the experimental setup minimizing cross-mapping rates. Moreover, Crossmapper can be used for resource optimization in sequencing facilities by pooling different samples into one sequencing library. AVAILABILITY AND IMPLEMENTATION: Crossmapper is a command line tool implemented in Python 3.6 and available as a conda package, allowing effortless installation. The source code, detailed information and a step-by-step tutorial is available at our GitHub page https://github.com/Gabaldonlab/crossmapper. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
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