Commit a360a180 authored by Slaheddine Kastalli's avatar Slaheddine Kastalli
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Update README.md

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# DADA2 pipeline
DADA2 is a Snakemake workflow based on dada2 (Callahan and al., 2016) and FROGS (Escudié and al, 2018) method which consists of a series of steps to filter the raw sequences obtained through Illumina sequencing. The final step aims to obtain the taxonomy of the sequences that have been filtered in order to study the microbial community.
DADA2 is a Snakemake workflow based on dada2 (Callahan and al., 2016) and FROGS (Escudié and al, 2018) methods which consists of a series of steps to filter the raw sequences obtained through Illumina sequencing. The final step aims to obtain the taxonomy of the sequences that have been filtered in order to study the microbial community.
Running DADA2 consists on calling a single command from the command line.
The output data format include biom format, phyloseq objets and R data sets.
## Getting ready
......@@ -67,4 +67,4 @@ At this point you have all the data needed to run the pipeline.
./RunSnake.sh global.smk
```
* The config file (in json format) is read by Snakemake to determine the inputs, steps, arguments and outputs.
* All raw data (usually fastq gziped files) need to be in one directory (DATA).
\ No newline at end of file
* All raw data (usually fastq gziped files) need to be in one directory (DATA).
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