Hi Everyone !
I just released the first version of my master thesis project, AllMine, a flexible pipeline for allele mining.
You can use AllMine to discover de novo Single Nucleotide Polymorphism (SNPs) onto next generation sequencing data of various types (RNAseq, WGS, RRGS ect.). AllMine working principle is to compare your sequencing data to a annotated reference sequence to call SNPs. By defining target regions onto your reference sequence, your can extract specific SNPs and discover allele polymorphism. AllMine also perform SNPs phasing. AllMine was developed for HPC environments using Snakemake and Slurm.
Returns and suggestions are greatly appreciated and will be taken into account for later versions.
Link to the project: https://github.com/tbersez/Allmine
Full documentation at: https://allmine.readthedocs.io/en/latest/?badge=latest
Thanks for reading,