Now Published

Species-wide genomics of kākāpō provides tools to accelerate recovery

Kākāpō Genome Data

NCBI Kākāpō Taxonomy ID

Genome Availability

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.

Other Data Availability

Kākāpō data is available through the DOC and it is possible to request it here: https://data.agdr.org.nz/

Methods

00_Assembly_Procedures

Downloads the assembly. Assembly from NCBI is already masked, although we may want to identify repeats for use in the publication.

01_QC: QC & Adapter Trimming

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.

02_Alignments_to_Reference

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.

03_Reference_SNPs

FreeBayes, DeepVariant, and GATK.