@@ -13,7 +13,7 @@ OTU-clustering steps are based on [TARA Fred's metabarcoding pipeline](https://g
## Method
The wofklows processes raw data from fastq inputs (FastQC), merges paired-end reads together (vsearch), applies complex demultiplexing based on notice provided by the sequencing platform, primer clipping (cutadapt), sample dereplication (vsearch), sequencing quality extraction, clusters sequences in OTU (swarm), detects chimera (vsearch) and assign taxonomy to each OTU (NCBI taxonomy; ecotag; obitools). Ultimately, OTU tables with and without taxonomy assignments are generated. See the output documentation for more details.
The wofklows processes raw data from fastq inputs (FastQC), merges paired-end reads together (vsearch), applies complex demultiplexing based on notice provided by the sequencing platform, primer clipping (cutadapt), sample dereplication (vsearch), sequencing quality extraction, clusters sequences in OTU (swarm), detects chimera (vsearch) and assigns taxonomy to each OTU (NCBI taxonomy; ecotag; obitools). Ultimately, OTU tables with and without taxonomy assignments are generated. See the output documentation for more details.
## Workflow
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@@ -44,21 +44,12 @@ The wofklows processes raw data from fastq inputs (FastQC), merges paired-end re
We thank the following people for their help in the development of this pipeline:
* Agnes Duhamet
* Alice Valentini
* Apolline Gorry
* Bastien Mace
* David Mouillot
* Emilie Boulanger
* Laetitia Mathon
* Laura Benestan
* Stephanie Manel
* Tony Dejean
> Agnes Duhamet, Alice Valentini, Apolline Gorry, Bastien Mace, David Mouillot, Emilie Boulanger, Laetitia Mathon, Laura Benestan,Stephanie Manel, Tony Dejean
## Contributions and Support
:bug: If you are sure you have found a bug, then by all means submit a bug report. You can submit your bug reports on Gitlab [here](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_swarm/-/issues).
:bug: If you are sure you have found a bug, please submit a bug report. You can submit your bug reports on Gitlab [here](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_swarm/-/issues).
