CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies
Visualitza/Obre
10.1093/bioinformatics/btz626
Inclou dades d'ús des de 2022
Cita com:
hdl:2117/345929
Tipus de documentArticle
Data publicació2020
EditorOxford University Press
Condicions d'accésAccés obert
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continguts d'aquesta obra estan subjectes a la llicència de Creative Commons
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Reconeixement-NoComercial 3.0 Espanya
Abstract
Motivation
Numerous 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.
Results
Using 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.
CitacióHovhannisyan, H. [et al.]. CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies. "Bioinformatics", 2020, vol. 36, núm. 3, p. 925-927.
ISSN1367-4803
1460-2059
1460-2059
Versió de l'editorhttps://academic.oup.com/bioinformatics/article/36/3/925/5544929
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