Commit 1b1319fd authored by peguerin's avatar peguerin
Browse files

readme update

parent 8b8df8a4
......@@ -18,7 +18,7 @@ git clone https://github.com/Grelot/seaConnect--dDocent.git
* [snakemake](https://snakemake.bitbucket.io)
## Dependencies
You will need to have the following programs installed on your computer.
You will need to have the following programs installed on your computer. Alternatively we provide a singularity container (see below).
- OSX or GNU Linux
- bash 4.4.19
......@@ -42,6 +42,7 @@ You will need to have the following programs installed on your computer.
- GNU parallel
- seqtk 1.0
- BWA 0.7.17
- _(optional)_ [DEMORT 0.2.4](https://pypi.org/project/demort/0.2.4/)
## Singularity
......@@ -50,7 +51,7 @@ See https://www.sylabs.io/docs/ for instructions to install Singularity.
We provide a [Singularity recipe](Singularity.seaconnect) and ready to run container with all required dependencies.
### Build a container
Build a local container with all required programs and dependencies using Singularity recipe [Singularity.seaconnect](Singularity.seaconnect)
Build a local container as administrator with all required programs and dependencies using Singularity recipe [Singularity.seaconnect](Singularity.seaconnect)
```
sudo singularity build seaconnect.simg Singularity.seaconnect
......@@ -153,15 +154,27 @@ This command process demultiplexing for each `{lane}`. Results are stored into `
:warning: If your cleaned fastq data folder is not into the current directory, you have to create a binding point for the singularity container. Modify the `--singularity-args "-B /entrepot:/entrepot"` argument of the command below.
## _(optional)_ DEmultiplexing MOnitoring Report Tool
If you want a blacklist of `{sample}` fastq files with low coverage, you can use [DEMORT](https://pypi.org/project/demort/0.2.4/) to get number of reads by `{sample}` fastq files.
```
bash 00-scripts/demort.sh {species}
```
This command evaluates demultiplexed fastq files by computing various metrics. `{sample}` with a low number of reads are blacklisted. Results are stored into [98-metrics](98-metrics) folder.
## Mapping `{barcode}` with `{pop}` and `{sample}`
Each fastq file belonging to a specific `{barcode}` is renamed by the corresponding association `{pop}` and `{sample}` as stipulated into `{species}_sample_information.tsv` file. (see for instance [mullus_sample_information.tsv](01-infos/mullus_sample_information.tsv))
```
bash 00-scripts/rename.sh {species} 01-infos/{species}_sample_information.csv
bash 00-scripts/rename.sh {species} 01-infos/{species}_sample_information.csv 98-utils/{species}_samples_blacklist.txt
```
This command create a symlink of all fastq files such as `03-samples/{lane}/sample_{barcode}.fq.gz` is linked by `04-ddocent/{species}/{pop}_{sample}.F.fq.gz`.
:paperclip: Optionally, if a samples blacklist is provided, blacklisted {sample} is filtered.
## dDocent workflow
......
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