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Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring

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A bit more shifting has to be done till for the 21 #metabarcoding primer sets to be tagged and tested = ) A Levenshtein distance of 1-2 bp means the primers are too similar -> Tagswitching can happen! scripts and more info in this related @PeerJPreprints: https://t.co/tIDCoCc29e https://t.co/KOm08QCFWL
RT @VascoElbrecht: Update of our scaling up #metabarcoding @PeerJPreprints is online! =) some minor improvements + new example sample layou…
36 days ago
RT @VascoElbrecht: Update of our scaling up #metabarcoding @PeerJPreprints is online! =) some minor improvements + new example sample layou…
Update of our scaling up #metabarcoding @PeerJPreprints is online! =) some minor improvements + new example sample layout that does use a unique primer combination for each replicate. Thanks to Arne Beermann from @leeselab for the suggestion! https://t.co/tIDCoCc29e https://t.co/9LUp8RyKyg
Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring https://t.co/we2ltjAECx
37 days ago
Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring https://t.co/R4YV4H5oPF
117 days ago
RT @VascoElbrecht: Updated @PeerJPreprints! Finally: better fusion #metabarcoding BF2+BR2 primer versions now available (the P7 we used so…
RT @VascoElbrecht: Updated @PeerJPreprints! Finally: better fusion #metabarcoding BF2+BR2 primer versions now available (the P7 we used so…
RT @metabar_papers: Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring https://t.co/h1E32gm4FB
118 days ago
RT @metabar_papers: Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring https://t.co/h1E32gm4FB
118 days ago
Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring https://t.co/fuVTWZNdUV
Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring https://t.co/h1E32gm4FB
Updated @PeerJPreprints! Finally: better fusion #metabarcoding BF2+BR2 primer versions now available (the P7 we used so far at @leeselab were not ideal, but did still work). I also did add a few hints on how to set things up with indexing for 1000+ samples https://t.co/tIDCoCc29e https://t.co/gFnTNxvO8g
@MatSeymour @BangorUniPress @alpineedna @NERCscience Hey mat, great. Write me a pm if you need details/ me to look over things. There is also a new (untested) BF3 primer i can send you under the counter. Also https://t.co/YIxDCZ9cG1 might be helpful. Minor update soon, with tagging 1000+ samples and updated P5 (cured one is false).
RT @VascoElbrecht: here is your weekend read: Scaling up #metabarcoding for monitoring macroinvertebrates! Practical guide to @illumina fus…
RT @VascoElbrecht: here is your weekend read: Scaling up #metabarcoding for monitoring macroinvertebrates! Practical guide to @illumina fus…
RT @VascoElbrecht: here is your weekend read: Scaling up #metabarcoding for monitoring macroinvertebrates! Practical guide to @illumina fus…
RT @VascoElbrecht: Updated version of our workflow manuscript now available @PeerJPreprints: Further improved tags and added analysis tools…
Updated version of our workflow manuscript now available @PeerJPreprints: Further improved tags and added analysis tools for Levenshtein distance to catch indels that might affect the tags! https://t.co/tIDCoCc29e
Happy to inform you that an updated version of the manuscript is live, solving the issues with the not ideal designed tags and adding Levenshtein distance analysis to account for indels in tags! https://t.co/Pvm6G6PMSD apologies again for overlooking this initially!
162 days ago
RT @VascoElbrecht: here is your weekend read: Scaling up #metabarcoding for monitoring macroinvertebrates! Practical guide to @illumina fus…
RT @VascoElbrecht: here is your weekend read: Scaling up #metabarcoding for monitoring macroinvertebrates! Practical guide to @illumina fus…
RT @VascoElbrecht: here is your weekend read: Scaling up #metabarcoding for monitoring macroinvertebrates! Practical guide to @illumina fus…
191 days ago
RT @VascoElbrecht: here is your weekend read: Scaling up #metabarcoding for monitoring macroinvertebrates! Practical guide to @illumina fus…
RT @VascoElbrecht: here is your weekend read: Scaling up #metabarcoding for monitoring macroinvertebrates! Practical guide to @illumina fus…
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Supplemental Information

Figure S1: Newly developed fusion primer sets (BF2+BR2), suitable for tagging 288 individual wells

DOI: 10.7287/peerj.preprints.3456v4/supp-1

Figure S2: Base composition of the inline tagging region

DOI: 10.7287/peerj.preprints.3456v4/supp-2

Figure S3: Hamming distance between tags for all fusion primers

DOI: 10.7287/peerj.preprints.3456v4/supp-3

Figure S4: Levenshtein distance between tags for all fusion primers

DOI: 10.7287/peerj.preprints.3456v4/supp-4

Script S1: R script used for randomly generating inline barcodes for the given primer sets (includes visualization, as shown in Figure S3 and Figure 3)

DOI: 10.7287/peerj.preprints.3456v4/supp-5

Table S1: Table providing an overview of proposed tagging combinations (as shown in Figure 3)

DOI: 10.7287/peerj.preprints.3456v4/supp-6

Manuscript file for providing feedback

(Pleas use track changes)

DOI: 10.7287/peerj.preprints.3456v4/supp-7

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Vasco Elbrecht conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Dirk Steinke authored or reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

primer sequences and scripts to generated them are provided as supporting information

Funding

V.E. and D.S. are supported by funding through the Canada First Research Excellence Fund. This work represents a contribution to the ‘Food From Thought’ research program and the EU Action ‘DNAqua-Net’ (CA15219). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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