ABYSS Assembly Output
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11 days ago
Tom Brady • 0

I have a project where I'm to compare some seq data from some non model eukaryotic species. I'm trying to assemble some short read data (2x150, PE), and I'm getting crappy results from AByss (used kmer size 96). Is there anything I can do to get a higher N50 value. Eventually I want to mask repeats and annotate with BRAKER so I can compare with OrthoFinder.

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Assembly abyss • 389 views
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When you assemble a large eukaryotic genome from short reads, you will inevitably get a small N50 (unless you use linked reads like 10x, see https://en.wikipedia.org/wiki/Linked-read_sequencing). To make a decent assembly, you need either long reads (Nanopore or Pacbio) or at least linked short reads.

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Also, you can try some other short read assemblers, for example, Platanus or MaSuRCA. However, N50 will probably not be much larger than what you had with ABySS.

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Should I try to optimize the kmer size? Or would it also not make that much of difference either?

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Yes, trying several k-mer sizes will probably result in a better assembly.
For example, you can try k-mer sizes from 21 to 141 with step 10. Or, find the optimal k-mer size with KmerGenie and assemble with only this k-mer size.

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