SPAdes

[hoelzer]

Main citation:

@Article{Bankevich:12,
  author  = {Bankevich, Anton and Nurk, Sergey and Antipov, Dmitry and Gurevich, Alexey A and Dvorkin, Mikhail and Kulikov, Alexander S and Lesin, Valery M and Nikolenko, Sergey I and Pham, Son and Prjibelski, Andrey D and Pyshkin, Alexey V and Sirotkin, Alexander V and Vyahhi, Nikolay and Tesler, Glenn and Alekseyev, Max A and Pevzner, Pavel A},
  title   = {{SPAdes}: a new genome assembly algorithm and its applications to single-cell sequencing.},
  journal = {J Comput Biol},
  year    = {2012},
  volume  = {19},
  number  = {5},
  pages   = {455--477},
  doi     = {10.1089/cmb.2012.0021},
  pmid    = {22506599},
  url     = {http://dx.doi.org/10.1089/cmb.2012.0021},
}

but in some context, we also like to cite

@article{Nurk:17,
  title={meta{SPA}des: a new versatile metagenomic assembler},
  author={Nurk, Sergey and Meleshko, Dmitry and Korobeynikov, Anton and Pevzner, Pavel A},
  journal={Genome Res},
  volume={27},
  number={5},
  pages={824--834},
  year={2017},
  publisher={Cold Spring Harbor Lab}
}

Question: how to achive this with our current system when only having one bib file per tool?

[replikation]

we cant put both in one file? I would put multiple citations that correspond to one tool in one file. Or is this an issue @hoelzer

[hoelzer]

@replikation No this is no problem (see busco.bib for example). However, SPAdes is an example of a tool where one wants to cite Bankevich et al. in general and in addition Nurk et al. if used in --meta mode.

When we put both into the spades.bib then both citations will always occur in the bib file.

[replikation]

mh tricky, perhaps separate dir for this? - but how do we "auto cite" this clever?

[hoelzer]

We could have workflow-dependent dirs (maybe subdirs in bibs).

Let's say we have a hybrid dir and add a spades.bib including only Nurk et al. to the hybrid dir. Then we pass another parameter (hybrid) to the cite.sh that can then also collect literature from this workflow-dependent sub-dir.

So when cite.sh is called w/o any additional parameters it will only check for literature in the main bibs directory. When additional parameters are provided cite.sh checks for sub-dirs and when they exist for matching bib files.

For rnaSPAdes (https://academic.oup.com/gigascience/article/8/9/giz100/5559527) we could then have another subfolder rnaseq again with a spades.bib that only holds this citation.

What do you think? I just want to avoid that things get too complicated.

[replikation]

• but then one dir for "special cases" might be enough or?

[replikation]

• you can decide what feels more convenient - clean; with less annoyance

[hoelzer]

• but then one dir for "special cases" might be enough or?

Unfortunately not, see the metaSPAdes/rnaSPAdes case :) but likely there are only very few such cases. I will suggest something