Assembly of Phylogenomic Datasets from High-Throughput Sequencing data
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Updated
Aug 2, 2024 - Python
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…
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