Species-wide genomics of kākāpō provides tools to accelerate recovery
The Kākāpō genome is published through the Vertebrate Genomes Project and is available from NCBI: Kākāpō Genome 7 Sept 2018 The Primary assembly is used in these scripts.
Kākāpō data is available through the DOC and it is possible to request it here: https://data.agdr.org.nz/
Downloads the assembly. Assembly from NCBI is already masked, although we may want to identify repeats for use in the publication.
In QC Folder
Adapter Trimming, base quality trimming, and merging performed FASTP and with AdapterRemovalV2. FastQC is run on both pre-processed (MultiQC_1) and post-processed (MultiQC_2). QC Results are be available on Google Drive. Right click and select "Download" then open the downloaded file.
BWA Mapping to align each lane of sequencing to the reference genome. Samples are renamed to the bird name + lane number. MultiQC report generated for alignment statistics is available on Google Drive.
FreeBayes, DeepVariant, and GATK.