@@ -96,7 +96,8 @@ For each genome you need to provide a database name (which **can't** contain spa
>The path to the index files **should include the basename** of the index, _(e.g: ./resources/databases//Human/Homo\_sapiens\_h38)_
>Thus, the index files _(Homo\_sapiens\_h38.bt2, Homo\_sapiens\_h38.2.bt2, etc.)_ are found in a folder named **'Homo\_sapiens\_h38'**
>If, for example, the Bowtie, Bowtie2 and BWA indices of a given genome reside in the **same folder**, a **single** path may be provided to **all** the of indices
>For example, the Bowtie, Bowtie2 and BWA indices of a given genome reside in the **same folder**
>A **single** path may be provided to **all** the of indices
The index used will be the one compatible with the chosen aligner _(as specified using the --aligner option)_
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@@ -110,18 +111,18 @@ It's suggested including genomes and sequences that:
For IRD_U233_TransVIHMI, cretaed this indexes:
-**Human**: main sources of lab. contaminations _(exepted if Boston Dynamics Atlas robot did the job)_ **not included**
-**Mouse**: main model in biology experimentation, very frequent in NGS facility core **not included**
-**Arabidopsis**: frequent plant model in NGS facility core associated with plants researches (IRD, CIRAD, INRAE, ...) **not included**
-**Human**: main sources of lab. contaminations _(exepted if Boston Dynamics Atlas robot did the job)_ **¡not included!**
-**Mouse**: main model in biology experimentation, very frequent in NGS facility core **¡not included!**
-**Arabidopsis**: frequent plant model in NGS facility core associated with plants researches (IRD, CIRAD, INRAE, ...) **¡not included!**
-**Ecoli**: frequent bacteria model, also an indicator of human contaminations, also in feces and stool samples
-**PhiX**: usefull control in Illumina sequencing run technology
-**Adapters**: use for libraries generation
-**Vector**: use in general molecular biology
-**Gorilla**: species studied in TransVIHMI **not included**
-**Chimpanzee**: species studied in TransVIHMI **not included**
-**Bat**: species studied in TransVIHMI **not included**
-**Gorilla**: species studied in TransVIHMI **¡not included!**
-**Chimpanzee**: species studied in TransVIHMI **¡not included!**
-**Bat**: species studied in TransVIHMI **¡not included!**
