Methods for De-novo Genome Assembly

Arash Bayat; Hasindu Gamaarachchi; Nandan P. Deshpande; Marc R. Wilkins; Sri Parameswaran

doi:10.20944/preprints202006.0324.v1

Comment 1

Received: 3 July 2020
The commenter has declared there is no conflict of interests.

Comment: The article seems a bit out of date. It is becoming clearer in 2020 that 2nd generation (NGS) short reads will soon be superseded by long reads from PacBio and Oxford Nanopore (if ONT can deliver full phasing as PacBio now can do). It is likely that Illumina will will not exist in 5 years.

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Response 1 to Comment 1

Received: 7 July 2020
Commenter:

Arash Bayat

Commenter's Conflict of Interests: I am an author

Comment: I agree with you that long-reads play a critical role in the de-novo assembly of complex genomes. Yet short-reads can be used for error correction of noisy long-reads. A significant part of the paper is dedicated to this combination (Hybrid Assembly). Apart from the scope of this paper, short-reads are yet the main data source for the reference-guided assembly pipeline (i.e. Variant-Calling).

I also agree with you that we have considered well-established tools (you mentioned out of date) but not the cutting edge new technologies. The paper is novel in terms of providing a uniform dataset and computational resources to evaluate the existing de-novo contig assembly tool in a fair environment considering both accuracy and runtime. We compare tools that are widely used by bioinformaticians so that the comparison result become useful for them to decide which pipeline they would like to use based on their specific requirement.

Many thanks for your comment on our paper.

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Methods for De-novo Genome Assembly

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