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A smaller alternative to NA12878 assembly?

Hi all, I am a bioinformatics newbie slightly constrained with time and need to quickly test an established scaffolding pipeline, bionano-solve using a small assembly dataset. Upon reading the documentation the pipeline was validated with NA12878 of the human genome. I was wondering if there are smaller benchmarks for which I can use its assembly to test the pipeline, please?

Thank you very much for your generous support.

assembly next-gen genome
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updated by h.mon h.mon • written by 65460clo • 65460clo

1 answer

You don't say what kind of data you have, if any, nor the requirements of the genome you want to use as benchmark. I suppose you want a high quality, finished genome? Then look at Saccharomyces cerevisae (12Mb haploid genome size) or Drosophila melanogaster (140Mb haploid genome size) genomes - it is likely you can obtain DNA from the same strains used to build the reference genome.

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written by h.mon h.mon

There is a reference is to bionano-solve so this would likely be Bionano Genomics data. This technology is based on optical mapping and not sequencing.

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written by GenoMax GenoMax

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