Unable to figure out code segments responsible for "De Novo Assembly"

NCGG-MGC / IMSindel

IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis

https://www.nature.com/articles/s41598-018-23978-z

MIT License

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Unable to figure out code segments responsible for "De Novo Assembly" #15

Closed amansinha-sw closed 3 years ago

amansinha-sw commented 3 years ago

I am trying to understand the whole algorithm for this project. But I have not been able to find the "De Novo assembly of unmapped reads" code segments. Please help me with the details.

holrock commented 3 years ago

Hi, IMSindel don't perform De novo assembly. Consensus sequence is made from unmapped reads using mafft.

amansinha-sw commented 3 years ago

I was referring the publication below: Shigemizu, D., Miya, F., Akiyama, S. et al. IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis. Sci Rep 8, 5608 (2018). https://doi.org/10.1038/s41598-018-23978-z And it was unclear where exactly you were using the "De Novo Assembly". Thanks for clarifying.