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May I suggest the following genomes which often are used as outgroups or as supplemental information in various biological analyses:

Genomes are available either at GenomeArk or ensembl.org

Model species:
Drosophila melanogaster
Mouse Mus musculus
Human Homo sapiens
Rat Rattus norvegicus
S. cerevisiae Saccharomyces cerevisiae
Zebrafish Danio rerio
Chicken Gallus gallus
Tropical clawed frog Xenopus tropicalis
C. elegans Caenorhabditis elegans

Evolutionary outgroups:
Coelacanth Latimeria chalumnae
Elephant shark Callorhinchus milii
Hagfish Eptatretus burgeri
Spotted gar Lepisosteus oculatus
Northern pike Esox lucius
Lamprey Petromyzon marinus
Atlantic cod Gadus morhua

Possible representatives for each of the major vertebrate lineages:
Lineage Species name Common name Order
Amphibian Bufo bufo common toad Anura
Amphibian Geotrypetes seraphini Gaboon caecilian Gymnophiona
Birds Aquila chrysaetos chrysaetos european golden eagle Accipitriformes
Birds Sterna hirundo common tern Charadriiformes
Cartilaginous Scyliorhinus canicula lesser-spotted catshark Carcharhiniformes
Cartilaginous Pristis pectinata smalltooth sawfish Pristiformes
Cartilaginous Amblyraja radiata Thorny skate Rajiformes
Fish Pygocentrus nattereri Red-bellied piranha Characiformes
Fish Antennarius maculatus warty frogfish Lophiiformes
Mammal Pipistrellus pipistrellus common popistrelle Chiroptera
Mammal Tachyglossus aculeatus short-beaked ehidna Monotremata
Mammal Sciurus carolinensis grey squirrel Rodentia
Reptile Thamnophis elegans Western terrestrial garter snake Squamata
Reptile Gopherus evgoodei Goode's thornscrub tortoise Testudines

All the best,
Monica Solbakken

[ /cluster/shared/databases/blast]$ du -hs 2021-05-27
951G 2021-05-27
[/cluster/shared/databases/blast]$ du -hs 2021-07-01
462G 2021-07-01

The 2021-07-01 version is about half the expected size. Which indicates an connection failure/time out during the download

Initial sheep assembly (Oar_v3.1) of the Texel breed reference genome was published by the International Sheep Genomics Consortium. Oar_v3.1
https://www.sheephapmap.org/
This version was published in Science in 2014 from the sequence of a Texel animal. The fully annotated genome is available via ENSEMBL, NCBI and UCSC. http://www.ensembl.org/Ovis_aries_rambouillet/Info/Strains?db=core

Oar_v4.0 https://www.ncbi.nlm.nih.gov/assembly/585171

Goat reference genome https://www-ncbi-nlm-nih-gov.ezproxy.uio.no/assembly/GCF_001704415.1/

Expected output

Running SPAdes on 13 genes
time parallel --eta -j 4 spades.py --only-assembler --threads 1 --cov-cutoff 8 --12 {}/{}_interleaved.fasta -o {}/{}_spades :::: spades_genelist.txt > spades.log

Computers / CPU cores / Max jobs to run
1:local / 8 / 4

If Error:
time parallel --eta -j 4 spades.py --only-assembler --threads 1 --cov-cutoff 8 --12 {}/{}_interleaved.fasta -o {}/{}_spades :::: spades_genelist.txt > spades.log
parallel: Error: Command line too long (118 >= 0) at input -12: gene079

real 0m0.237s

Need to include this to use the tool bowtie2

Hi :)

It would be useful for my research group to have the following added (both are on Ensembl):

common carp (common_carp_genome, INSDC Assembly GCA_000951615.2):
http://ftp.ensembl.org/pub/release-104/fasta/cyprinus_carpio/

goldfish (ASM336829v1, INSDC Assembly GCA_003368295.1):
http://ftp.ensembl.org/pub/release-104/fasta/carassius_auratus/

I saw in your reply to Monica that you wanted more information than the name, so if you need more than the information above just let me know.

Thanks!

Sjannie