README.md

mito_ma: Scripts and data for the project on mtDNA evolution in yeast hybrid MA lines

Directory contents:

nanopore_assemblies.ipynb

Notebook file for nanopore assembly and annotation of parental mtDNAs

assembly_comparison.ipynb

Notebook file for comparison of nanopore mtDNA assemblies with previously published illumina mtDNA assemblies lines.

divergence.iynb

Notebook file for computation of parental evolutionary divergence (nuclear and mtDNA) of the MA crosses

nj_trees.ipynb

Notebook file for neighbor-joining phylogenetic trees of individual mtDNA features

mito_ma.ipynb

Notebook file for analysis of mtDNA recombination, mtDNA deletion, respiration, and aneuploidies in MA

make_liftover.py

Script to produce liftover tables from mugsy pairwise whole-genome alingments. Used to confirm marker variants and analyze long read assemblies from MA lines.

mtDNA_assemblies/

Direcrtory containing mtDNA assemblies (.fasta), processed annotations (.gff), and raw MFannot outputs (.new, .new.sqn, .new.tbl) for the 13 parental strains of the MA crosses.