search

TobyBaril / EarlGrey

Earl Grey: A fully automated TE curation and annotation pipeline
Other
139 stars 20 forks source link

Low coverage datasets? #15

Closed AntonioBaeza closed 2 years ago

AntonioBaeza commented 2 years ago

Hello, I wonder how you expect to be the performance of EarlGrey with low coverage datasets and how it might compare with RepeatExplorer2? Thank you.

TobyBaril commented 2 years ago

Hi, Thanks for checking out Earl Grey. I am not overly familiar with RepeatExplorer2, but as far as I understand it is designed for repeat identification from sequencing reads, rather than an assembled genome. Earl Grey has been designed to annotate TEs in genome assemblies (ie a genome file in fasta format), rather than from sequencing reads. I think in this case RepeatExplorer2 is still the best option for repeat identification in the absence of an assembled genome.