Genomic diversity of Elm trees (Ulmus species)

This repo shares scripts used to analyze whole-genome sequences of elms.

SNP-density plot for elm samples using CMplot.

For the details about the project, please see the project page at the Center for Forest Protection.

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• Check the checksum of downloaded files using ‘md5sum’ or similar
• Run FASTQC on raw files for quality control
• Trim the raw files using Trimmomatic, FASTP or Cutadapt.
• Run FASTQC on trimmed files.
• Run MultiQC to aggregate FASTQC results into a single HTML file (raw and trimmed separately) for better visualization. Check the “Sequence GC content”, “Overrepresented sequences”, “Adapter Content”, etc. Exclude erroneous sample(s).
• Map the raw reads against the reference genome, Ulmus americana GCA_010015005.3 using BWA version 2 ‘mem’ algorithm.