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Assessing intraspecific genetic diversity from community DNA metabarcoding data

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RT @VascoElbrecht: Happy with the automated haplotype plots =) JAMP update soon! White= sample does not contain the OTU, numbers = OTU, bl…
Happy with the automated haplotype plots =) JAMP update soon! White= sample does not contain the OTU, numbers = OTU, blue and other colors = haplotype. details in the @PeerJPreprints https://t.co/TIdFcq5bOc https://t.co/XNmghbStAu
RT @VascoElbrecht: What a great present for Easter = ) Our @thePeerJ manuscript on #metabarcoding based haplotyping has been accepted! Than…
479 days ago
RT @VascoElbrecht: What a great present for Easter = ) Our @thePeerJ manuscript on #metabarcoding based haplotyping has been accepted! Than…
RT @VascoElbrecht: What a great present for Easter = ) Our @thePeerJ manuscript on #metabarcoding based haplotyping has been accepted! Than…
480 days ago
RT @VascoElbrecht: What a great present for Easter = ) Our @thePeerJ manuscript on #metabarcoding based haplotyping has been accepted! Than…
What a great present for Easter = ) Our @thePeerJ manuscript on #metabarcoding based haplotyping has been accepted! Thank you so much @leeselab, @dirch3, reviewers, and editors
RT @VascoElbrecht: New revised version of our @PeerJPreprints online: #metabarcoding based haplotyping. Should hopefully be soon accepted a…
489 days ago
RT @metabar_papers: Estimating intraspecific genetic diversity from community DNA metabarcoding data https://t.co/ghQIjnUOzq
RT @VascoElbrecht: New revised version of our @PeerJPreprints online: #metabarcoding based haplotyping. Should hopefully be soon accepted a…
RT @VascoElbrecht: New revised version of our @PeerJPreprints online: #metabarcoding based haplotyping. Should hopefully be soon accepted a…
RT @metabar_papers: Estimating intraspecific genetic diversity from community DNA metabarcoding data https://t.co/ghQIjnUOzq
RT @metabar_papers: Estimating intraspecific genetic diversity from community DNA metabarcoding data https://t.co/ghQIjnUOzq
490 days ago
RT @VascoElbrecht: New revised version of our @PeerJPreprints online: #metabarcoding based haplotyping. Should hopefully be soon accepted a…
490 days ago
RT @VascoElbrecht: New revised version of our @PeerJPreprints online: #metabarcoding based haplotyping. Should hopefully be soon accepted a…
RT @VascoElbrecht: New revised version of our @PeerJPreprints online: #metabarcoding based haplotyping. Should hopefully be soon accepted a…
RT @VascoElbrecht: New revised version of our @PeerJPreprints online: #metabarcoding based haplotyping. Should hopefully be soon accepted a…
490 days ago
Estimating intraspecific genetic diversity from community DNA metabarcoding data https://t.co/6ovfRZ5Bly
RT @VascoElbrecht: New revised version of our @PeerJPreprints online: #metabarcoding based haplotyping. Should hopefully be soon accepted a…
RT @VascoElbrecht: New revised version of our @PeerJPreprints online: #metabarcoding based haplotyping. Should hopefully be soon accepted a…
New revised version of our @PeerJPreprints online: #metabarcoding based haplotyping. Should hopefully be soon accepted at @thePeerJ *fingers crossed* Find the manuscript v3 here: https://t.co/HcvWDxT72O (Also new extensive JAMP package documentation added on github)! https://t.co/salV0DNaAf
490 days ago
RT @metabar_papers: Estimating intraspecific genetic diversity from community DNA metabarcoding data https://t.co/ghQIjnUOzq
Estimating intraspecific genetic diversity from community DNA metabarcoding data https://t.co/ghQIjnUOzq
RT @metabar_papers: Assessing intraspecific genetic diversity from community DNA metabarcoding data https://t.co/WwdtC3SMsi
531 days ago
Assessing intraspecific genetic diversity from community DNA metabarcoding data https://t.co/5Z4HcjcNcu
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Supplemental Information

Figure S1: Schematic overview of errors affecting metabarcoding data and clustering / denoising strategies to reduce them

DOI: 10.7287/peerj.preprints.3269v1/supp-1

Figure S2: Effect of different quality filtering (may ee) on reads of the singe species mock sample

DOI: 10.7287/peerj.preprints.3269v1/supp-2

Figure S3: Effect of different alpha values in read denoising of the singe species mock sample

DOI: 10.7287/peerj.preprints.3269v1/supp-3

Figure S4: Detailed plots of four example taxa from the denoised monitoring samples, showing haplotype maps & networks, similarity between replicates and sequence alignment for all BF/BR primer sets

DOI: 10.7287/peerj.preprints.3269v1/supp-4

Figure S5: Overview of the haplotyping strategy used here and their implementation in the JAMP R package

DOI: 10.7287/peerj.preprints.3269v1/supp-5

Table S1: Finland haplotype table (for all 4 different primer combinations)

DOI: 10.7287/peerj.preprints.3269v1/supp-6

Scripts S1: Metabarcoding and denoising pipeline, and additional scripts used to produce the figures

DOI: 10.7287/peerj.preprints.3269v1/supp-7

Manuscript work file for providing feedback

Please use track changes / comment functions. Thank you for your feedback.

DOI: 10.7287/peerj.preprints.3269v1/supp-8

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

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

Ecaterina Edith Vamos conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.

Dirk Steinke wrote the paper, reviewed drafts of the paper.

Florian Leese conceived and designed the experiments, wrote the paper, reviewed drafts of the paper.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

Haplotype sequences are available in supporting Table S1

Data Deposition

The following information was supplied regarding data availability:

Raw data is already available in SRA (NCBI), see SRR5295658, SRR5295659, SRR4112287

Bioinformatic package is available on GitHub:

github.com/VascoElbrecht/JAMP

Funding

This study is part of the European Cooperation in Science and Technology (COST) 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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