Published October 29, 2024
| Version v1
Dataset
Open
Comparative Genomics of Triturus Balanced Lethal System Version 1.0
Authors/Creators
-
1.
Leiden University
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2.
Naturalis Biodiversity Center
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3.
Jagiellonian University
- 4. Institute for Biological Research "Siniša Stanković" National Institute of the Republic of Serbia, University of Belgrade
- 5. University of Belgrade Faculty of Biology
- 6. University of Belgrade, Faculty of Biology
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7.
University of Kentucky
Description
This repository details the bioinformatic pipelines used to investigate the comparative genomics of the balanced lethal system found in Triturus newts
Linkage maps for Triturus and Lissotriton are available in the file: Triturus and Lissotriton Linkage Maps.xlsx
The sequences of all targets captured in the study are available in the file: triturusTargetsV1Oneliners_7139unique.fasta
The associate publication is available on BioRxiv: https://doi.org/10.1101/2024.10.29.620207
The raw data is available via NCBI: bioproject - PRJNA1175462
The study is broken into 6 sections (combined into the .zip file Triturus_Lethal_Evolution-1.00) - each of which contains a detailed readme in its respective folder:
The following software was employed for this study:
Perl v3.38.0
R v4.4
BBtools v38.96
Trimmomatic v0.39
SAMtools v1.18
GATK v4.5.0.0
VCFtools v0.1.16
BCFtools v1.18
BLAST+ v2.14.1
Lep-MAP3 v.0.5
nQuire (cloned from commit 8975c94)