Daphnia pulex assembly version 1.0 (February 2011)
From Ensembl: https://metazoa.ensembl.org/Daphnia_pulex/Info/Index
Assembly:
ftp://ftp.ensemblgenomes.org/pub/metazoa/release-44/fasta/daphnia_pulex/dna/Daphnia_pulex.V1.0.dna.toplevel.fa.gz
Annotation:
ftp://ftp.ensemblgenomes.org/pub/metazoa/release-44/gff3/daphnia_pulex/Daphnia_pulex.V1.0.44.gff3.gz

Daphnia magna assembly version daphmag2.4 (April 2010)
From Ensembl: http://metazoa.ensembl.org/Daphnia_magna/Info/Index?db=core
Assembly:
ftp://ftp.ensemblgenomes.org/pub/metazoa/release-44/fasta/daphnia_magna/dna/Daphnia_magna.daphmag2.4.dna.toplevel.fa.gz
Annotation:
ftp://ftp.ensemblgenomes.org/pub/metazoa/release-44/gff3/daphnia_magna/Daphnia_magna.daphmag2.4.44.gff3.gz

Next steps:

• Create HELP ticket containing user's email send to Ann and link it to this one (it will still be protected)
• Google search to see if more recent assemblies can be found.

I found this paper that appears to be a newer, better version for Daphnia magna, but I don't know if the data can be obtained:

• The genome of the freshwater water flea Daphnia magna: A potential use for freshwater molecular ecotoxicology Link: https://www.researchgate.net/publication/330313926_The_genome_of_the_freshwater_water_flea_Daphnia_magna_A_potential_use_for_freshwater_molecular_ecotoxicology

Depending on above, create a new ticket for assembling the Quickload files for the two Daphnias:

BED-detail file with:

• Human-friendly text functional annotations in field 14
• Gene name in field 13
• Transcript name in field 4

Two-bit file with genome sequence

• Reference sequence names should match reference sequence names used in BED-detail file above

genome.txt file with reference sequences and sizes from 2bit file above

• Reference sequences should be listed in a user-friendly order; depends on how the sequences are named and the completeness of the genome

Also, if the genome(s) are very much in fragments and there are tens of thousands of sequences per assembly, we need to do some filtering to screen out reference sequences that lack annotations or are extremely small. This requires some research to find out how many is too many – i.e., how long does it take the gene models to load into IGB.

Thanks Nowlan! I have added some new parts of the task. If you are able to take this on, I would appreciate it!

If not, un-assign it move it to Sprint 11.

The paper: The genome of the freshwater water flea Daphnia magna: A potential use for freshwater molecular ecotoxicology links out to both an assembly (NCBI PRJNA490418) and annotation (GenBank SRP161660), but the annotation does not appear to have been uploaded .

As the user mentioned the Ensembl files, I think it would be best to start with those as they have both assembly and annotation available for Daphnia magna and pulex genomes. This more recent Daphnia magna genome could be added in the future if the annotation can be found.

Suggestion:

• Contact the authors of the newer paper and tell them we would like to feature their new genome in Integrated Genome Browser.
• Ask them when they are planning to upload the annotations file.
• Encourage them to do it soon! And let them know we would be grateful if they would do it in bed-detail format rather than GFF

My guess is they are still struggling with the evil horror that is GFF

Also let them know we are collaborating with the Galaxy project and are hoping also to feature their new genome in the Galaxy project system.

If we do that, then everybody in the world can start using Galaxy to work with their genome.

I think that if we do that, they will be very happy because their work will get cited more?

Also, we could include all the versions, possibly?

Thank you for doing this!

This type of thing is hugely time-consuming, and it really requires someone with a PhD and tons of experience to do it. (Yourself.)

I emailed the contact person for the paper - Professor Jae-Seong Lee (slee2@skku.edu) to ask if he could provide the annotation file.

His lab also has a JBrowse site set up to view the Daphnia Magna assembly and annotation. While I cannot access the data itself, JBrowse does allow downloading a gff of each linkage group (there are 10 linkage groups in addition to ~hundreds of scaffolds). This could be a way to at least get the linkage group annotations.

Please allow your computer to mirror "Data Management for Quickload" Dropbox folder.
Once it is mirrored on your machine, please add the new folders to the checked-out svn repository there - it is in the folder "genomes"
Edit the contents.txt file you see there to include the new genome versions.
Once everything is there, I will be able to commit it to the repository.

Regarding the species.txt file:

• Please edit the corresponding files in the IGB code base so that when we do a new release of IGB, the new version will pick up the new genome version synonyms.

Sorry, I forgot this request:

• Please update .htaccess in Quickload as well

Added the four Daphnia assemblies and annotations to "Data Management for Quickload" Dropbox folder. Updated contents.txt. I modified the .htaccess.

I did not modify the species.txt or synonyms.txt in the dropbox folder. I created the pull request IGBF-1883-AddDaphnia with modifications to the IGB codebase species.txt and synonyms.txt (core/synonym-lookup/src/main/resources/species.txt and core/synonym-lookup/src/main/resources/synonyms.txt). Tested in IGB and the species/synonyms appeared to be working correctly.

PR merged.