Commit ef553596 authored by peguerin's avatar peguerin
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readme update

parent 501c7173
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**eDNA-seq Metabarcoding OTU-clustering** is specifically used for the analysis of environmental DNA metabarcoding NGS data, demultiplexing, filtering and clustering sequences in Operational Taxonomic Unit (OTU).
This pipeline has been initially tested with marine environment samples, using molecular markers such as Teleo1. The workflow should work with any organisms and environment. It is proven for large-scale data analysis.
This pipeline has been initially tested with marine environment samples, using molecular markers such as Vert01 ([Riaz et al. 2011](https://doi.org/10.1093/nar/gkr732)), Teleo01 ([Valentini et al. 2016](https://doi.org/10.1111/mec.13428)), Chond01 or Mamm01 ([Taberlet et al. 2018](https://doi.org/10.1093/oso/9780198767220.001.0001)). The workflow should work with any organisms and environment. It is proven for large-scale data analysis.
OTU-clustering steps are based on [TARA Fred's metabarcoding pipeline](https://github.com/frederic-mahe/swarm/wiki/Fred%27s-metabarcoding-pipeline).
## 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 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.
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, trims primers (cutadapt), dereplicates sequences (vsearch), extracts sequencing quality values, clusters sequences in OTU (swarm), detects and removes 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.
OTU-clustering steps are based on [TARA Fred's metabarcoding pipeline](https://github.com/frederic-mahe/swarm/wiki/Fred%27s-metabarcoding-pipeline).
## Workflow
......@@ -65,7 +66,7 @@ You can cite the **eDNA-seq Metabarcoding OTU-clustering** publication as follow
>
> *Virginie Marques, Pierre‐Edouard Guerin, Mathieu Rocle, Alice Valentini, Stephanie Manel, David Mouillot, Tony Dejean*
>
> Molecular Ecography. 2020 Aug 04. doi: https://doi.org/10.1111/ecog.05049.
> Ecography. 2020 Aug 04. doi: https://doi.org/10.1111/ecog.05049.
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