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Guide through code for a Minimmap2 genome alignment and a seq-seq-pan pan-genome alignment with visualizations in R. The tutorial presents an example using two haplotypes of the optix locus in Heliconius butterflies.

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StevenVB12/Tutorial_pan_genomics

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ATAC
ATAC
 
 
Minimap2_out
Minimap2_out
 
 
TEs
TEs
 
 
gene_annotation
gene_annotation
 
 
seq-seq-pan_out
seq-seq-pan_out
 
 
sequences
sequences
 
 
Plot_minimap_alignment.R
Plot_minimap_alignment.R
 
 
Plot_pan_genome.R
Plot_pan_genome.R
 
 
README.md
README.md
 
 
genome_list.txt
genome_list.txt
 
 
seq-seq-pan_bedfile_conservation.py
seq-seq-pan_bedfile_conservation.py
 
 
seq-seq-pan_bedgraph_chrompos.py
seq-seq-pan_bedgraph_chrompos.py
 
 
seq-seq-pan_blocks_intervals.py
seq-seq-pan_blocks_intervals.py
 
 
seq-seq-pan_toFasta.py
seq-seq-pan_toFasta.py
 
 

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Guide through code for a Minimmap2 genome alignment and a seq-seq-pan pan-genome alignment with visualizations in R. The tutorial presents an example using two haplotypes of the optix locus in Heliconius butterflies.

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