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Old 07-21-2019, 11:47 AM   #1
tamu_anand
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Default heavily used bionformatics software without publications

Hi all

I am curious to know from the Bioinformatics/Genomics/CompBio research community about popular or heavily used software that are not published?

In my opinion, BBTools from DOE JGI is one of those tools which are not published in journals.

I am sure there are many others depending on the specific research area that the researcher is working on.

You might be asking "what's the motive behind the question" - I generally feel that the research community is very hesitant to adopt tools that are not published AND/OR just published in preprint servers like bioRxiv (e.g. Salmon-SA method).

Take for example the Salmon-SA method referenced above - it would eventually get published soon in peer-reviewed publications. While some researchers are convinced to use the method based on the information in the preprint many others are skeptical to use it till it has been published.

I wanted to know the thoughts of the research community on the above.

Thanks in advance.
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Old 07-21-2019, 12:16 PM   #2
GenoMax
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At least one tool from BBTools suite is published. Here is the paper for BBMerge.

It is my understanding that BBTools were originally developed for internal use at JGI. JGI subsequently allowed Brian to make the software available for others to use.

It is more the case of journals not looking favorably on tools only papers. Even though "bwa" is published, "bwa mem" was thought not enough to justify a new paper of its own (I believe by journals and not Heng Li). Here is the biostars thread that discussed this. Everyone's favorite NGS QC program "fastqc" has not been published (and may never be) but it still has become the de facto standard package everyone uses.

Last edited by GenoMax; 07-21-2019 at 12:24 PM.
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Old 07-21-2019, 08:03 PM   #3
robp
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Hi tamu_anand,

I think this is an interesting question, and one that I'm not certain has a clearly "right" or "wrong" answer. While peer-review and publication of the paper associated with a method can be important for many reasons, the utility (or correctness or accuracy) of the method is obviously independent of that event. Also, while I can understand why some might use the existence of a "published" paper as a filter for considering the use of a method, I personally consider it neither necessary nor sufficient. GenoMax brings up the prototypical example (but it's a great one) of BWA-mem. Generally, my filter for deciding to use a tool or not is based upon understanding, at some level, what it is doing and also testing it, if reasonable data is available for doing that.

It's also worth pointing out that salmon, like many genomics tools, functions as a platform for research. This means that new ideas and approaches are explored quite frequently, and when they seem useful, they are often exposed to users. The more thoroughly the features are tested, the more prominent they become. Sometimes, as in the case of SA, the tool developers choose to write a manuscript about them. Other times, however, the features may become available but not be accompanied by any manuscript. In such cases, it's my belief in the utility of the feature / improvement and not the publication status of any associated manuscript that primarily determines if I will use it. Otherwise, I might be missing out on useful or important features while waiting for a manuscript that may never come.
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Old 07-22-2019, 09:09 AM   #4
tamu_anand
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Thanks GenoMax and RobP for your valuable inputs.

RobP - I totally agree with you on all you have said - the most important being the last bullet below:
  1. my filter for deciding to use a tool or not is based upon understanding, at some level, what it is doing and also testing it, if reasonable data is available for doing that.
  2. in the case of SA, the tool developers choose to write a manuscript about them. Other times, however, the features may become available but not be accompanied by any manuscript.
  3. missing out on useful or important features while waiting for a manuscript that may never come.
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Old 07-31-2019, 03:51 AM   #5
colindaven
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Freebayes, the SNV caller, is another heavily used tool with just a preprint.

From the github site:
"
A preprint Haplotype-based variant detection from short-read sequencing provides an overview of the statistical models used in freebayes. We ask that you cite this paper if you use freebayes in work that leads to publication. This preprint is used for documentation and citation. freebayes was never submitted for review, but has been used in over 1000 publications.
"

However, remember, pre publication peer review is NOT a guarantee of software quality. Remember, we are all peer reviewers, and we review a tool every time we check out a tool and its docs, use it, test, and report results.
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Old 08-01-2019, 04:22 PM   #6
dcameron
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Picards tools has no paper or preprint.
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Old 08-09-2019, 06:47 AM   #7
tamu_anand
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Thanks Colindaven and dcameron for your inputs - very much appreciated.
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Old 08-11-2019, 12:36 PM   #8
finswimmer
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bwa mem
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Old 08-11-2019, 09:45 PM   #9
SeqGeq
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SeqGeq is one to check out.
Webinars:
www.flowjo.com/learn/webinars

Documentation:
docs.flowjo.com/seqgeq

Download:
www.flowjo.com/solutions/seqgeq/downloads
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