I had a collaborator ask me to write up my analysis for the methods section of a paper, and I explicitly described each step, including software tools, version numbers, and citations for each one.

I found out that the version he submitted to the journal kept the text the same but removed all citations to the tools, despite them being critical to doing the analyses

Imagine if you spent years working out tedious details of an important problem in the field, implementing them in an easy-to-use and well-documented way, and someone uses your exact method and doesn't reference your work.

In any other context, that would be some form of academic misconduct

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You need to reference these things in your papers.

Not only for reproducibility of your work (version numbers are very important), but to give credit to those authors for their hard work

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Nearly every single genomics paper requires sequence alignment, and I can't count the number of times I've seen Bowtie or BWA mentioned in the text and no citation is provided.

These are some of the best software tools in bioinformatics available today, and people use them because of their thoroughness, flexibility, and ease of use.

Those things takes years and years to perfect, and that work deserves recognition

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