## Jan 22, 2025
## Edmundo Torres-Gonzalez

Mitochondrial DNA (mtDNA) assemblies for human and non-human primates (NHP) intended for a CACTUS alignment to obtain a sequence reconstruction of the ancestral genomes.

I included individual fasta files and a guide tree for bonobo, chimp, human, gorilla, S. orangutan, BB. orangutan, and siamang.These genomes are small (~16 Kb) so I expect jobs would run relatively quickly. 

The main issue I could foresee would be due to the circularity of mtDNA genomes and how they are represented linearly in assemblies. Therefore, I included two additional modified versions of the assemblies in case the linear representation of mtDNA genomes would cause funny business at the ends (near the breakpoint). 

The directories contain three versions of the same assemblies:

1) standard

The standard release version of mtDNA assemblies. NHP mtDNA assemblies were obtained from T2T v1 assemblies (as they are currently excluded from v2). 
For human, I included the rCRS ("revised Cambridge Reference Sequence") mtDNA assembly, commonly used in the field. The human assembly was modified, moving the breakpoint in the linear sequence by 577 bp, to better align with assemblies from the other species.


2) shifted

The breakpoint was shifted by 8400 bp to diagnose potential misalignments at the ends of the original breakpoint. This is useful when mapping reads to mtDNA but might not affect a CACTUS alignment.


3) doubled

The "standard" assembly but duplicated and concatenated. Also useful when mapping reads to mtDNA but not necessarily  useful here.