Hi all,
Basically my goal is to 'genotype' 1500 loci in salmon through sequencing. Had initially though of RAD/GBS/ddRAD/etc, however then I realised that one can in theory just do targeted amplicon sequencing with this number of targets. Ultra-high multiplexing with Ampliseq or Truseq custom enrichment seem feasible, however all the assay design tools seem oriented to humans. In theory I could probably multiplex 1000 samples per lane and get 100x coverage of my regions on the Hiseq and also get very efficient sequencing with Proton, but:
1. No targeted enrichment/amplicon kits seem to offer more than 96 barcodes
2. All the assay design tools seem to be for human genome sequence only.
In principle I can't see any reason why Ampliseq couldn't be used in this case if we had the sequence available...or am I missing something here?
Has anyone else had experience with sequencing of 1000+ amplicons in animals/plants with high level multiplexing/barcoding?
Cheers,
Matt
Basically my goal is to 'genotype' 1500 loci in salmon through sequencing. Had initially though of RAD/GBS/ddRAD/etc, however then I realised that one can in theory just do targeted amplicon sequencing with this number of targets. Ultra-high multiplexing with Ampliseq or Truseq custom enrichment seem feasible, however all the assay design tools seem oriented to humans. In theory I could probably multiplex 1000 samples per lane and get 100x coverage of my regions on the Hiseq and also get very efficient sequencing with Proton, but:
1. No targeted enrichment/amplicon kits seem to offer more than 96 barcodes
2. All the assay design tools seem to be for human genome sequence only.
In principle I can't see any reason why Ampliseq couldn't be used in this case if we had the sequence available...or am I missing something here?
Has anyone else had experience with sequencing of 1000+ amplicons in animals/plants with high level multiplexing/barcoding?
Cheers,
Matt
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