Analysis for the manuscript "Eukaryotic adaptation to years-long starvation resembles that of bacteria"
Genome assebly and ploidy reconstruction
Tabulate raw reads
Trim sequence reads
Inspect sequence data quality
Denovo assembly with Celera
Denovo assembly with Platanus
Make blobplots
Select Celera results based on blobplots
Assembly statistics
Determine ploidy with Smudgeplot
Chromosome coverage in 404 and 402 compared to SefAle
Get coverage of the wild type genome by 404,424 and SelAle reads
Plot coverage of each chromosome to study the extand of ploidy change
SNP calling
Functional annotation of wild type genome
Get TOR1 sequences in each sample
Gain and loss of heterozygocity, Shared and unique polymorphism, in 404 and 424
Map 404 and 424 to SefAle genome
SNP call
Functional annotation of SefAle
Summarize polymorphisms
Synonymous and non synonymouse point mutations in descendant strains
Venn diagrams of share and unique genes genes with point mutation
Gain and Loss of heterozygocity
Summarize polymorphism types (for Figure-4C)