Commit 942981b9 authored by peguerin's avatar peguerin
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readme update

parent 77f33998
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[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![Snakemake](https://img.shields.io/badge/snakemake-5.5.2-brightgreen.svg)](https://snakemake.bitbucket.io)
Process Genotypage by Sequencing data with low coverage using a dDocent-based workflow. We performed this workflow as part of the project [SEACONNECT project](https://reefish.umontpellier.fr/index.php?article9/total-seaconnect) on 900 samples among 2 fish species _mullus Surmuletus_ and _diplodus Sargus_ in Mediterranean sea.
Process Genotypage by Sequencing data with low coverage using a dDocent-based workflow. We performed this workflow as part of the [SEACONNECT project](https://reefish.umontpellier.fr/index.php?article9/total-seaconnect) on 900 samples among 2 fish species _mullus Surmuletus_ and _diplodus Sargus_ in Mediterranean sea.
# INSTALLATION
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## Set up
**Wildcards :**
### Wildcards
* `{species}` : any complete project (in our case we have 2 projects : mullus and diplodus)
* `{lane}` : any physical lane on a flow cell that goes into the sequencing machine. We have many `{lane}` by `{species}`
* `{barcode}` : any DNA sequence attached to a reads which belong to a sample. We have many `{barcode}` by `{lane}` by `{species}`
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* `{sample}` : any sample
### Container
The container (see [Singularity](#singularity) section below) must be stored into the main directory of this project [seaConnect--dDocent](seaConnect--dDocent) with the name `seaconnect.simg`
The container (see [Singularity](#singularity) section below) must be stored into the main directory of this project [seaConnect--dDocent](.) with the name `seaconnect.simg`
### cleaned fastq data
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