Many references missing from the tail list

[dschigel]

Including in e.g. in this section.

Suggested action: cross-check of all references in the doc required: all bibliographic references in the text should be in the reference list, which should not have any references which are not found in the text.

[dschigel]

As discussed in Skype with @kcopas, I suggest we follow the basic principle that simple hyperlinks from the text do not require addition to the ref list. However, if the reference looks like bibliographic, or the link target is as doc with ISSN / ISBN, an addition is needed.

Example where no new reference needed in the tail list:

Furthermore, some fields from the GGBN standard and fields from the MIQE (minimum information for the publication of quantitative real-time PCR) guidelines for qPCR and ddPCR data have been included to make it applicable for a wide range of DNA-derived data.

Example where ref is missing and addition to the list is needed:

DNA-metabarcoding is used for samples originating from both terrestrial and aquatic environments, including water, soil, sediments, biofilms, plankton, bulk samples and faces, simultaneously identifying hundreds of species (Ruppert et al. 2019).

[dschigel]

Will do manual text to list check to start with

[dschigel]

To add to the reference list, respecting the target format and ordering (list below is not sorted)

• [x] - https://doi.org/10.1093/nar/gkj157
• [x] - http://dx.doi.org/10.1111/j.1471-8286.2007.01678.x
• [x] - https://doi.org/10.1016/j.gecco.2019.e00547
• [x] - https://doi.org/10.1111/eva.12882
• [x] - https://doi.org/10.1373/clinchem.2008.112797
• [x] - https://doi.org/10.1373/clinchem.2013.206375
• [x] - https://doi.org/10.1101/2020.04.27.063990
• [x] - https://doi.org/10.1098/rsbl.2008.0118
• [x] - https://doi.org/10.1002/edn3.89
• [x] - https://doi.org/10.1002/edn3.10
• [x] - https://doi.org/10.1007/s10750-017-3408-8
• [x] - https://doi.org/10.1186/2047-217X-1-7
• [x] - https://doi.org/10.1371/journal.pone.0066213

Not referred in the text biobliographically, add text references where relevant (preferred), or remove from reference list

• [x] 1. Bolyen, E., Rideout, J.R., Dillon, M.R. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 37, 852–857 (2019). https://doi.org/10.1038/s41587-019-0209-9
• [x] 2. Callahan B, McMurdie P & Holmes S (2017) Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. The ISME Journal 11: 2639–2643. https://doi.org/10.1038/ismej.2017.119
• [x] 3. Callahan, B., McMurdie, P., Rosen, M. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 13, 581–583 (2016). https://doi.org/10.1038/nmeth.3869
• [x] 4. Patrick D. Schloss, Sarah L. Westcott, Thomas Ryabin, Justine R. Hall, Martin Hartmann, Emily B. Hollister, Ryan A. Lesniewski, Brian B. Oakley, Donovan H. Parks, Courtney J. Robinson, Jason W. Sahl, Blaz Stres, Gerhard G. Thallinger, David J. Van Horn, Carolyn F. Weber. Applied and Environmental Microbiology Nov 2009, 75 (23) 7537-7541; DOI: 10.1128/AEM.01541-09
• [x] 5. Robert C. Edgar, Search and clustering orders of magnitude faster than BLAST, Bioinformatics, Volume 26, Issue 19, 1 October 2010, Pages 2460–2461, https://doi.org/10.1093/bioinformatics/btq461
• [x] 6. Panu Somervuo, Sonja Koskela, Juho Pennanen, R. Henrik Nilsson, Otso Ovaskainen, Unbiased probabilistic taxonomic classification for DNA barcoding, Bioinformatics, Volume 32, Issue 19, 1 October 2016, Pages 2920–2927, https://doi.org/10.1093/bioinformatics/btw346
• [x] 7. Frøslev, T.G., Kjøller, R., Bruun, H.H. et al. Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates. Nat Commun 8, 1188 (2017). https://doi.org/10.1038/s41467-017-01312-x
• [x] 8. Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. (2014) Swarm: robust and fast clustering method for amplicon-based studies. PeerJ 2:e593 doi: 10.7717/peerj.593

Overall formatting for the reference list is unsatisfactory, closing dots or not, first names spelled out or not etc. Careful checks desirable, but not critical to do before release: silent formatting / style improvements can be done on the go.

[thomasstjerne]

Most of the references in the numbered list are from this sentence where they are mentioned by the name of the tool/algorithm (hyperlinked to the DOI):

Several open source tools and algorithms exist for bioinformatic processing of metabarcoding data (QIIME2, DADA2, SWARM, USEARCH, Mothur, LULU, PROTAX).

1 - QIIME2 3 - DADA2 4 - Mothur 5 - USEARCH 6 - PROTAX 7 - LULU 8 - SWARM

Ref nr 2 on the list is mentioned in the sentence (as Callahan et al. 2017):

Availability of of all verified amplicon sequence variants (Сallahan et al. 2017) allow for precise reinterpretation of data

So please don´t remove those

[dschigel]

@thomasstjerne I agree to keep; each of them would need a bibliographic reference, not only a hyperlink - this is breaking the bibliographic standard. In my opinion it is ok to simply link out to a webpage, but it is no ok to omit a bibliographic reference when i) paper is found on the list but there is no obvious reference in the text and ii) other papers are referred to correctly. I can fix this, preserving 1, 3, 4, 5, 6, 7, 8. We are in sync here.

[dschigel]

Added missing references to the text, now every ref in the list has at least one ref from the text

[dschigel]

Added missing references to the list and fixed most horrible biobliographic formatting issues. A chance I overlooked some commas and spaces, to fix on the go.