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**_fusemblr_** is a pipeline wrapper designed for the assembly of complex genomes using nanopore reads and paired-end illumina
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**_fusemblr_** was designed for the <i>Fusarium oxysporum</i> assembly project (hence the name) <br/>
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The pipeline uses Nanopore (the longer and higher coverage the better); paired-end illumina reads and PacBio is optional <br/>
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The pipeline only requires Nanopore reads (the longer and higher coverage the better) and an estimation of genome size <br/>
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Paired-end illumina reads and PacBio is optional <br/>
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<i>Notably: Providing both illumina PacBio Hifi had very little impact on the resulting assemblies using our _Fusarium oxysporum_ datasets as we used recent ONT basecalled data, had high coverage and a good subset of long reads.</i>
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Following assembly it is recommended that you run [PAQman](https://github.com/SAMtoBAM/PAQman) on your resulting assembly to comprehensively check the quality <br/>
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It is recommended to feed your resulting assembly to PAQman alongside the 1.filtlong/*.fz.gz set of reads <br/>
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This can also help you compare any assemblies you have to check for the best.
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