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# Nanopore adaptive sampling to identify the NLR-gene family in melon (_Cucumis melo_ L.)
## Description
Repository to house all the scripts used in data analysis for the paper.
- ONT sequencing_summary.txt files for both runs (Anso-77 with Doublon; Chang-Bougi) are located in X.
- The functional annotation of the Anso-77 and Doublon genomes are in the X and X files.
###Background
Nanopore Adaptive Sampling (NAS) offers a promising approach for assessing genetic diversity in targeted genomic regions. Herein, we design and validate an experiment to enrich a set of resistance genes in several melon cultivars as a proof of concept.
###Results
We showed that each of the 15 regions we identified in two newly assembled melon genomes (subspecies melo) were successfully and accurately reconstructed as well as in a third cultivar from the agrestis subspecies. We obtained a fourfold enrichment, independently from the samples, but with some variations according to the enriched regions. In the agrestis cultivar, we further confirmed our assembly by PCR. We discussed parameters that can influence enrichment and accuracy of assemblies generated through NAS.
###Conclusions
Altogether, we demonstrated NAS as a simple and efficient approach to explore complex genomic regions. This approach finally unlocks the characterization of resistance genes for a large number of individuals, as required for breeding new cultivars responding to the agroecological transition.
To perform a complete analysis of the samples it is just necessary to run the bash script "launcher_analysis_NAS_standard.sh"
All the rest of scripts are launched by this one.
The .csv file list_runs with the information of each sample must be available in the working directory.
Multiple samples can be ran with a loop by adding their name next to the script name (sh NAS_launcher_analysis.sh SAMPLE1 SAMPLE2 ...)
Javier Belinchon-Moreno, Aurelie Berard, Aurelie Canaguier, Véronique Chovelon, Corinne Cruaud, Stéfan Engelen, Rafael Feriche-Linares, Isabelle Le-Clainche, William Marande, Vincent Rittener-Ruff, Jacques Lagnel, Damien Hinsinger, Nathalie Boissot, Patricia Faivre Rampant