Test dataset from: GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species
type: Dataset
distribution: Landing page for the dataset
description: This item contains a test dataset based on Sumatran rhinoceros (Dicerorhinus sumatrensis) whole-genome re-sequencing data that we publish along with the GenErode pipeline (https://github.com/NBISweden/GenErode; Kutschera et al. 2022) and that we reduced in size so that users have the possibility to get familiar with the pipeline before analyzing their own genome-wide datasets. We extracted scaffold ‘Sc9M7eS_2_HRSCAF_41’ of size 40,842,778 bp from the Sumatran rhinoceros genome assembly (Dicerorhinus sumatrensis harrissoni; GenBank accession number GCA_014189135.1) to be used as reference genome in GenErode. Some GenErode steps require the reference genome of a closely related species, so we additionally provide three scaffolds from the White rhinoceros genome assembly (Ceratotherium simum simum; GenBank accession number GCF_000283155.1) with a combined length of 41,195,616 bp that are putatively orthologous to Sumatran rhinoceros scaffold ‘Sc9M7eS_2_HRSCAF_41’, along with gene predictions in GTF format. The repository also contains a Sumatran rhinoceros mitochondrial genome (GenBank accession number NC_012684.1) to be used as reference for the optional mitochondrial mapping step in GenErode. The test dataset contains whole-genome re-sequencing data from three historical and three modern Sumatran rhinoceros samples from the now-extinct Malay Peninsula population from von Seth et al. (2021) that was subsampled to paired-end reads that mapped to Sumatran rhinoceros scaffold ‘Sc9M7eS_2_HRSCAF_41’, along with a small proportion of randomly selected reads that mapped to the Sumatran rhinoceros mitochondrial genome or elsewhere in the genome. For GERP analyses, scaffolds from the genome assemblies of 30 mammalian outgroup species are provided that had reciprocal blast hits to gene predictions from Sumatran rhinoceros scaffold ‘Sc9M7eS_2_HRSCAF_41’. Further, a phylogeny of the White rhinoceros and the 30 outgroup species including divergence time estimates (in billions of y…
modified: 2023-05-30T00:00:00Z
issued: 2022-08-25T00:00:00Z
publisher: Stockholm University
theme: HEAL
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Verena Kutschera
    type: Agent
    account: 0000-0002-8930-534X
    type: PrivateIndividual(s)
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Marcin Kierczak
    type: Agent
    type: PrivateIndividual(s)
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Tom van der Valk
    type: Agent
    account: https://orcid.org/0000-0001-6582-3452
    type: PrivateIndividual(s)
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Johanna von Seth
    type: Agent
    type: PrivateIndividual(s)
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Nicolas Dussex
    type: Agent
    account: https://orcid.org/0000-0002-9179-8593
    type: PrivateIndividual(s)
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Edana Lord
    type: Agent
    type: PrivateIndividual(s)
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Marianne Dehasque
    type: Agent
    type: PrivateIndividual(s)
qualified attribution: Attribution
  had role: principalInvestigator
  agent: David W. G. Stanton
    type: Agent
    type: PrivateIndividual(s)
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Payam Emami Khoonsari
    type: Agent
    type: PrivateIndividual(s)
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Björn Nystedt
    type: Agent
    type: PrivateIndividual(s)
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Love Dalén
    type: Agent
    type: PrivateIndividual(s)
qualified attribution: Attribution
  had role: principalInvestigator
  agent: David Díez del molino
    type: Agent
    account: https://orcid.org/0000-0002-9701-5940
    type: PrivateIndividual(s)
keyword: Bioinformatic methods development
keyword: Sequence analysis
keyword: Genomics

Landing page for the dataset
type: Distribution
title: Landningssida för datasetet @sv
access URL: Test dataset from: GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species
availability: stable

Stockholm University
type: Agent
name: Stockholms universitet @sv
type: Academia-ScientificOrganisation
source: 05f0yaq80