Dmitry Antipov
@dantipov.bsky.social
Genome assemblers and their friends. Postdoc at https://genomeinformatics.github.io/
In the average lab you develop a proof of concept level software to support your part of a research project and do it alone. So realistically only the version control would be clearly beneficial.
The thing is that even computational methods development labs often miss a lot of your points
The thing is that even computational methods development labs often miss a lot of your points
November 19, 2024 at 3:29 PM
In the average lab you develop a proof of concept level software to support your part of a research project and do it alone. So realistically only the version control would be clearly beneficial.
The thing is that even computational methods development labs often miss a lot of your points
The thing is that even computational methods development labs often miss a lot of your points
This post hurts a lot!
November 19, 2024 at 3:16 PM
This post hurts a lot!
TLDR:
Prolonged reviewing process may lead to situations when at least a part of a paper is clearly outdated and looks weird at the moment of publication.
And I do not know how this should be fixed, assuming that we cannot always make review iterations fast.
Prolonged reviewing process may lead to situations when at least a part of a paper is clearly outdated and looks weird at the moment of publication.
And I do not know how this should be fixed, assuming that we cannot always make review iterations fast.
March 14, 2024 at 12:38 AM
TLDR:
Prolonged reviewing process may lead to situations when at least a part of a paper is clearly outdated and looks weird at the moment of publication.
And I do not know how this should be fixed, assuming that we cannot always make review iterations fast.
Prolonged reviewing process may lead to situations when at least a part of a paper is clearly outdated and looks weird at the moment of publication.
And I do not know how this should be fixed, assuming that we cannot always make review iterations fast.
As a reader I would be happy if the journal would restart the reviewing process from scratch, with new reviewers. For all papers in progress, submitted too long (a year?) ago.
But as an author, I would be completely pissed off in such a situation.
But as an author, I would be completely pissed off in such a situation.
March 14, 2024 at 12:31 AM
As a reader I would be happy if the journal would restart the reviewing process from scratch, with new reviewers. For all papers in progress, submitted too long (a year?) ago.
But as an author, I would be completely pissed off in such a situation.
But as an author, I would be completely pissed off in such a situation.
Likely reviewers had some other questions and on the next round had no reasons to return to sections they already found to be OK. And authors were not encouraged to provide unrequested changes.
March 14, 2024 at 12:26 AM
Likely reviewers had some other questions and on the next round had no reasons to return to sections they already found to be OK. And authors were not encouraged to provide unrequested changes.
This is the answer. At September 2022 Verkko was already released and even preprint was published peer-reviewed; hifiasm was in process of adding the support for ONT.. No peer-reviewed publications for ONT+HiFi for both.
March 14, 2024 at 12:22 AM
This is the answer. At September 2022 Verkko was already released and even preprint was published peer-reviewed; hifiasm was in process of adding the support for ONT.. No peer-reviewed publications for ONT+HiFi for both.
So, one of two likely most popular tools in the field is completely ignored, and the other is run in the way it would produce clearly inferior assemblies! With no motivation in the text!
Junk paper? Bad reviewing quality?
None of the above!
Junk paper? Bad reviewing quality?
None of the above!
March 14, 2024 at 12:13 AM
So, one of two likely most popular tools in the field is completely ignored, and the other is run in the way it would produce clearly inferior assemblies! With no motivation in the text!
Junk paper? Bad reviewing quality?
None of the above!
Junk paper? Bad reviewing quality?
None of the above!
Ok, I can be biased about verkko, let's check hifiasm... Wow, it was run without ONT!
March 14, 2024 at 12:08 AM
Ok, I can be biased about verkko, let's check hifiasm... Wow, it was run without ONT!
Merfin is not an assembler, but I can understand what they mean. However, don't you feel that something is missing?
March 14, 2024 at 12:06 AM
Merfin is not an assembler, but I can understand what they mean. However, don't you feel that something is missing?
So, it is an Illumina+ONT based polishing pipeline, that is focused on diploid genomes and assumed to work after Flye assembler. Stated to be comparable or even better than state of the art HiFi "haplotype-resolved" assemblers. Pipeline itself looks decent, so I go directly to benchmarking..
March 14, 2024 at 12:04 AM
So, it is an Illumina+ONT based polishing pipeline, that is focused on diploid genomes and assumed to work after Flye assembler. Stated to be comparable or even better than state of the art HiFi "haplotype-resolved" assemblers. Pipeline itself looks decent, so I go directly to benchmarking..
Was not good in finding appropriate words. Of course it is not just "death", it is murder.
February 20, 2024 at 4:18 AM
Was not good in finding appropriate words. Of course it is not just "death", it is murder.
Ok, got your email, thank you! nice "practical" solution but still have questions
October 27, 2023 at 10:47 PM
Ok, got your email, thank you! nice "practical" solution but still have questions