Reference ITS1 and rps10 sequences for the mock community?

[peterjc]

I am having trouble compiling a complete set of reference sequences for your mock community, e.g. for Peronospora farinosa, grep "farinosa" oomycetedb_whole_2022_07_05_08_58_07.fa returns no no "farinosa" matches for rps10. That FASTA file was the 2021-03-01 first release with 885 entries downloaded from http://oomycetedb.cgrb.oregonstate.edu/search.html (but named according to when it was downloaded).

(I am aware of some name changes in the NCBI taxonomy, e.g. Pythium undulatum to Elongisporangium undulatum, and Pythium irregulare to Globisporangium irregulare)

Quoting https://github.com/grunwaldlab/rps10_barcode/blob/main/publication/reviewer_response.Rmd

"we knew all the organisms sequenced had a perfect match in both databases"

Are those sequences available? e.g. could you add two FASTA files to this repository, the ITS1 and rps10 sequences of your mock community. Thank you!

[peterjc]

I suspect the files I am hoping to see are its1_reference_db.fa and rps10_reference_db.fa and/or mock_comm_its1_sanger.fasta and mock_comm_rps10_sanger.fasta referenced here:

• https://github.com/grunwaldlab/rps10_barcode/blob/main/06--mock_community.Rmd
• https://github.com/grunwaldlab/rps10_barcode/blob/main/docs/06--mock_community.html
• https://grunwaldlab.github.io/rps10_barcode/06--mock_community.html