Templates and functions in Julia language to process next-generation sequencing (NGS) data for population genetic analysis.
ngsJulias receives NGS data files as input and provides routines and functions to parse files, perform data filtering and implement custom population genetic analyses.
Two implementations for analysing pooled sequencing data and polyploid genomes are further presented.
A publication describing the methodology and its implementation is available here. Full documentation is accessible here.
Please note that, at the moment, ngsJulia requires a reference sequence without N bases and it does not process indels longer than 9bp. Filter your data accordingly.
You can clone the repository with git clone https://github.com/mfumagalli/ngsJulia.git
We also provide two novel applications of ngsJulia for low-coverage short-read sequencing data.
- ngsPloidy infers the ploidy of samples from genotype likelihoods.
- ngsPool estimates allele frequencies (and more) from pooled-sequencing data.
Archived code and scripts to replicate all results in the accompanying paper are available the paper folder.