Genome assemblies and gene annotations for the 6 Bat genomes that were generated in the Bat1K Pilot project. 

Jebb D, Huang Z, Pippel M, Hughes GM, Lavrichenko K, Devanna P, ..., Hiller M #, Vernes SC #, Myers EW #, Teeling EC #.
Six new reference quality bat genomes illuminate the molecular basis and evolution of bat adaptations. 
submitted


The folder contains the 
- genome assembly (fasta format, gzipped)
- annotations of coding genes
for 6 bats:
  Greater horseshoe bat (Rhinolophus ferrumequinum): assembly HLrhiFer5
  Egyptian rousette (Rousettus aegyptiacus): assembly HLrouAeg4
  Pale spear-nosed bat (Phyllostomus discolor): assembly HLphyDis3
  Velvety free-tailed bat (Molossus molossus): assembly HLmolMol2
  Kuhl's pipistrelle (Pipistrellus kuhlii): assembly HLpipKuh2
  Greater mouse-eared bat (Myotis myotis): assembly HLmyoMyo6

There are also liftOver chains from and to previous Rousettus assemblies.

Gene annotations are provided in 3 formats
- UCSC's genePred format https://genome.ucsc.edu/FAQ/FAQformat.html#format9
- UCSC's bed 12 format https://genome.ucsc.edu/FAQ/FAQformat.html#format1
- gff3 (gzipped)

The folder intactIsoforms contains only transcripts which are intact (start and stop codon, no frameshift, no premature stop).
All transcripts are provided in the allAnnotatedIsoforms folder.

The AugustusModel folder contains the trained Augustus model for de novo gene predictions in bats.