Support multiple reference genomes

[suhas-r]

[red-t]

Hi everyone, great work on developing CoRAL!

I was wondering if it's possible to use a customized genome as the reference. For example, can I use GRCh38_not_alt.fa along with an additional fasta file, such as other.fa?

Thanks in advance!

[jluebeck]

Hi,

Thanks for this query. At the moment, non-atandard references will not be compatible. If other fasta entries were included, they would be ignored from analysis. We are hoping to resolve this limitation in future updates.

Thanks,
Jens

[red-t]

Hi,

Thanks for the answer. Just to clarify, does it mean that CoRAL cannot be used to detect chimeric amplifications, similar to what AA did in Fig. 4 of this paper?

Best,
Zhongren

[jluebeck]

Not yet, but it's in the works :)