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nf-core / eager

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Competitive mapping for strain separation

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EisenRa
EisenRa commented Jul 18, 2018

In some metagenomic contexts, there can be closely related species in a sample that can make read mapping to a single reference genome difficult (e.g. cross-mapping of reads between species). In this situation, it can be useful to employ competitive mapping, whereby reference genomes from closely related species are concatenated (in a multifasta), and the reads mapped to this reference. This can a

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