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virajbdeshpande / AmpliconArchitect

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.
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Long read sequencing + AA to call ecDNA? #102

Open alhafidzhamdan opened 3 years ago

alhafidzhamdan commented 3 years ago

Hi this might be off topic but have you tried using long read data on AA? I'm planning to generate HIFI reads for some of my samples and wonder if it's any good with AA? Probably not as HIFI won't have discordant reads, and if not, what would you recommend, and if you have any insights on this.

Thanks in advance! A

jluebeck commented 3 years ago

Hi,

We have not tested this before. However, because AA uses discordant read pairs to identify the presence of junctions (which are refined by split-reads), the absence of discordant read pairs from a single-end sequencing technology such as PacBio or ONT will likely result in missing breakpoints in the region of interest. Others have alternatively attempted de novo assembly approaches for long-read resolution of ecDNA structures, but keep in mind that if the read does not span multiple breakpoints in a complex amplicon, the assembly may contain errors or incomplete contigs. The incorporation of long-reads into AA is a project which is on our radar.

Best, Jens

alhafidzhamdan commented 3 years ago

Hi Jens,

Thanks for that. I guess what you are saying is that single-end sequencing will miss regions where an amplicon does not span multiple breakpoints hence may miss these. Do keep me updated if you end up developing such a tool to integrate/refine AA with long read data. Thanks Al