I posted my review verbatim, without any editing, and with the charge for the review laid out by the journal. Part of my goal was to provide some insight into why I was enthusiastic about Salmon, and why I reviewed it positively for publication.

Looking back on my review, I have a few thoughts - especially in light of Lior's hit piece and Rob et al's response.

First, it is always a pleasure reviewing software papers when you have used the tool for ages. My lab uses Salmon, trains people in running Salmon, and passes around blog posts and papers discussing Salmon results. I think we had been using Salmon for at least a year when I was asked to review the paper. So I was already pretty confident that Salmon performed well in general and I did not need to try to run it, evaluate it, etc.

Second, my review hit on a number of high points about Salmon: generally, that it was an important new tool of interest and that it was a significant improvement to the tried-and-tested Kallisto technique. More specifically, I felt that the GC bias correction was likely to be critical in the future (see esp the isoform switching observation!), and that the open-source license was an important aspect of the Salmon software. To my mind this meant that it warranted publication, a case I made succinctly but tried to make strongly.

Third, my review missed at least one very important aspect, which was the streaming nature of the Salmon implementation. The rebuttal covers this nicely...

Last, my review uses the term "pseudoalignment" and not "quasimapping." The distinction between these two terms is part of the brouhaha; but to my mind the basic idea of finding equivalence classes for reading mapping is pretty similar no matter what you call it, and it was clear (both from the citations to Kallisto and the discussion in the paper) that the core concept had been published as part of the Kallisto work. I don't think it matters what it's called - it's a good idea, I'm glad that there are multiple implementations that agree well with each other, and I think it was adequately, appropriately, and generously cited in the Salmon paper.

So, anyway, there are my thoughts. Yours welcome below!

(Before you comment, please do see the code of conduct for this blog - it's linked below. In particular, I place myself under no obligation to retain posted comments, and I will delete comments that are useless, or dishonest.)

--titus

Other articles

My Salmon review

Wed 16 August 2017
By C. Titus Brown

In science.

tags: salmon review

I was one of the reviewers of the Salmon paper by Patro et al., 2017, Salmon provides fast and bias-aware quantification of transcript expression. I was asked to review the paper on September 14, 2016, and submitted my review (or at least stopped getting reminders :) soon after October 20th.

The ...
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How to analyze, integrate, and model large volumes of biological data - some thoughts

Mon 15 May 2017
By C. Titus Brown

In science.

tags: ddd data integration

This blog post stems from notes I made for a 12 minute talk at the Oregon State Microbiome Initiative, which followed from some previous thinking about data integration on my part -- in particular, Physics ain't biology (and vice versa) and What to do with lots of (sequencing) data.

My ...
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A (revised and updated) shotgun metagenome workshop at UC Santa Cruz

Mon 24 April 2017
By C. Titus Brown

In teaching.

tags: metagenomics ngs workshop

We just finished teaching a second version of our two-day shotgun metagenome analysis workshop, this time at UC Santa Cruz (the first one was in October 2016, at Scripps Institute of Oceanography). Harriet Alexander led the workshop and Phillip Brooks and I co-taught; Luiz Irber, Shannon Joslin, and Taylor Reiter ...
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Workshops posted for DIBSI - July 10-15, July 17-21
Tue 18 April 2017
By C. Titus Brown

In training.

tags: ngs swc

As part of our Summer Institute in Data Intensive Biology, we will be running nine week-long computational workshops from July 10 to July 17 at the University of California, Davis.

Week 1: July 10-15
- Genome Wide Association Study Workshop - Tamer Mansour and Erica Scott
- Undergraduate Curriculum Hackathon
- Introduction to Python ...
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Registration reminder for our two-week summer workshop on high-throughput sequencing data analysis!

Fri 17 March 2017
By C. Titus Brown

In training.

tags: ngs-course ngs swc

Our two-week summer workshop (announcement, direct link) is shaping up quite well, but the application deadline is today! So if you're interested, you should apply sometime before the end of the day. (We'll leave applications open as long as it's March 17th somewhere in the world.)

Some ...
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My thoughts for "Imagining Tomorrow's University"

Wed 15 February 2017
By C. Titus Brown

In science.

tags: futureuni

So I've been invited to Imagining Tomorrow's University, and they have this series of questions they'd like me to answer.

(Note that you can follow the conversation at #TomorrowsUni on Twitter.)

Conveniently I already answered many of these questions in my "What is Open Science?" blog post ...
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