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Inexperiencedresearcher avatar Inexperiencedresearcher commented on June 20, 2024 1

Thank you for your reply, I have tried changing it to -orientation and it works.

also, I tried multi-k assembly + scaffolding (I managed to increase my storage) and it all works, but I have yet to check whether the scaffolding with BESST has improved the asssemblies at various k values.

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rchikhi avatar rchikhi commented on June 20, 2024

hi, yes please try this change, but also if you have only paired-end reads, you could also just skip scaffolding or pre-merge pairs if they're overlapping. Assembly result shouldn't be drastically different.

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rchikhi avatar rchikhi commented on June 20, 2024

your assembly is already in the file assembly_k41.contigs.fa and you can consider it to be the final result of the pipeline (without scaffolding)

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