### General information

Author: Verena Kutschera
Contact e-mail: generode@nbis.se
DOI: 10.17044/scilifelab.19248172
License: GPL 3.0 +
This readme file was last updated: 22-02-2022

Please cite as: Verena E. Kutschera, Marcin Kierczak, Tom van 
der Valk, Johanna von Seth, Nicolas Dussex, Edana Lord, Marianne 
Dehasque, David W. G. Stanton, Payam Emami, Björn Nystedt, 
Love Dalén, David Díez-del-Molino (2022). Test dataset from: 
GenErode: a bioinformatics pipeline to investigate genome 
erosion in endangered and extinct species. 
DOI 10.17044/scilifelab.19248172

### Dataset description

Files included into this repository:

- reference.tar.gz: sumatran_rhino_22Jul2017_9M7eS_haploidified_headersFixed_Sc9M7eS_2_HRSCAF_41.fasta 
with scaffold ‘Sc9M7eS_2_HRSCAF_41’ from the Sumatran 
rhinoceros genome assembly (Dicerorhinus sumatrensis harrissoni; 
GenBank accession number GCA_014189135.1). 
GCF_000283155.1_CerSimSim1.0_genomic.Sc9M7eS_2_HRSCAF_41.fasta 
with three scaffolds from the White rhinoceros genome assembly 
(Ceratotherium simum simum; GenBank accession number GCF_000283155.1; 
‘NW_004454182.1’, ‘NW_004454248.1’, and ‘NW_004454260.1’). 
GCF_000283155.1_CerSimSim1.0_genomic.Sc9M7eS_2_HRSCAF_41.gtf 
contains gene predictions from the three White rhinoceros scaffolds 
in GTF format. 
rhino_NC_012684.fasta with a Sumatran rhinoceros mitochondrial 
genome (GenBank accession number NC_012684.1).

- historical.tar.gz: FASTQ files with paired-end reads from three 
historical Sumatran rhinoceros samples from the now-extinct Malay 
Peninsula population that had mapped to the 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 two of the 
historical Sumatran rhinoceros samples, three sequencing libraries 
are available per sample that had been sequenced on two lanes each. 
For the third historical sample, 24 sequencing libraries are 
available that had been sequenced on two lanes (12 libraries per 
lane). SRA identifiers: JvS008 (SR08) ERS4044060, 
JvS009 (SR09) ERS4044061, JvS022 (SR22) ERS4044063.

- modern.tar.gz: FASTQ files with paired-end reads from three 
modern Sumatran rhinoceros samples from the now-extinct Malay 
Peninsula population that had mapped to the 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 each of 
the three modern Sumatran rhinoceros samples, one sequencing 
library is available. SRA identifiers: JvS033 (KB6196) ERS4042484, 
JvS034 (KB6197) ERS4042485, JvS035 (KB6198) ERS4042486.

- gerp_outgroups.tar.gz: gzipped FASTA files with scaffolds from the 
genome assemblies of mammalian outgroup species for GERP analyses 
that contained genes with reciprocal blast hits to genes from the 
Sumatran rhinoceros scaffold ‘Sc9M7eS_2_HRSCAF_41’. 
Included species and GenBank accession numbers of genome assemblies: 
Ailurus fulgens GCA_002007465.1, Antilocapra americana GCA_007570785.1, 
Balaenoptera acutorostrata GCF_000493695.1, Bubalus bubalis 
GCF_003121395.1, Camelus dromedarius GCF_000803125.2, Canis lupus 
GCF_014441545.1, Catagonus wagneri GCA_004024745.2, Cervus elaphus 
GCA_002197005.1, Diceros bicornis GCA_013634535.1, Enhydra lutris 
GCF_002288905.1, Equus asinus GCA_016077325.1, Giraffa camelopardalis 
GCA_017591445.1, Hippopotamus amphibius GCA_004027065.2, 
Hyaena hyaena GCF_003009895.1, Leptonychotes weddellii GCF_000349705.1, 
Lipotes vexillifer GCF_000442215.1, Manis javanica GCF_014570535.1, 
Mesoplodon bidens GCA_004027085.1, Ovis aries GCF_002742125.1, 
Panthera leo GCA_008795835.1, Paradoxurus hermaphroditus GCA_004024585.1, 
Physeter catodon GCF_002837175.2, Procyon lotor GCA_015708975.1, 
Spilogale gracilis GCA_004023965.1, Suricata suricatta GCF_006229205.1, 
Tapirus indicus GCA_004024905.1, Tragulus javanicus GCA_004024965.2, 
Tursiops truncatus GCF_011762595.1, Ursus maritimus GCF_017311325.1, 
Zalophus californianus GCF_009762305.2

- gerp_tree.nwk: Phylogeny of the White rhinoceros and the 30 
mammalian outgroup species including divergence time estimates 
(in billions of years) from timetree.org in NEWICK format.

- config.tar.gz: Configuration and metadata files used to analyze 
this test dataset with the GenErode pipeline, results presented 
in Kutschera et al. (2022): 
config_mitogenomes.yaml: configuration file used to run the 
mitochondrial mapping step. 
config_sum_rhino.yaml: configuration file used to run GenErode 
using the Sumatran rhinoceros scaffold as reference genome. 
config_whi_rhino.yaml: configuration file used to run GenErode 
using the White rhinoceros scaffolds as reference genome. 
rhino_3_historical_samples.txt: metadata file for historical 
samples. 
rhino_3_modern_samples.txt: metadata file for modern samples.


To analyze this dataset with GenErode, please download this 
repository and uncompress all folders in a dedicated directory. 
The configuration and metadata files in `config/` can be used as 
examples for GenErode runs. Instructions on how to run the 
GenErode pipeline are provided in the GitHub repository 
(https://github.com/NBISweden/GenErode/wiki).


References:

Kutschera VE, Kierczak M, van der Valk T, von Seth J, Dussex N, 
Lord E, et al. GenErode: a bioinformatics pipeline to investigate
genome erosion in endangered and extinct species. bioRxiv. 2022.
doi: 10.1101/2022.03.04.482637