Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

Repo accompanying our manuscript on quantifying extra-nuclear inserts from population-level low-pass sequencing data

QC and filtering of genome skims, followed by organelle assembly and/or genome analysis

get chloroplast and mitochondrial genes from contigs of genome-skimming or transcriptome data

#Scripts to create Kraken2 database of PAFTOL V2.0 Angio353 genes. An excellent database for taxonomic identification of plants. #https://treeoflife.kew.org/ #https://github.com/DerrickWood/kraken2/wiki #Prior to using this script, download and install kraken2 and make sure it is working and in your PATH. #Make sure the location of the python sc…