Addition of reference genome: Phoenix dactylifera

custom-genome
database

#1

Could you please add the phoenix dactylifera reference genome for rnaseq analysis?
Thank you


#2

There are two versions of the genome at NCBI:
https://www.ncbi.nlm.nih.gov/assembly/organism/42345/latest/

Is there another source? We can consider it have a preference to index only publicly released genomes.

This prior Q&A explains how to make a genome request and how to use any genome now as a Custom reference genome with tools.


#3

Yes both version are ok. Kindly include one of them in galaxy server reference genome list.
Custom reference genome is complicated we are unable to do. Thank you


#4

A custom reference genome is just an uploaded fasta file. Sometimes it needs to be run through the NormalizeFasta tool for some simple reformatting but beyond that, not much else is needed.

We won’t be adding any new genomes for a bit longer (we are restructuring the data repository), so I encourage you to try this.


#5

Actually, when I look closer at the NCBI assembly projects, neither has a set of chromosomes/contigs for the genome available. The first has the Chloroplast and Mitochondrial organelles assembled plus some scaffolds for genome (too many to use effectively as a “genome” target with NGS tools like mappers). The second just has WGS reads (unplaced/organized).

Without even a partially assembled genome, there is no reference assembly to use as a Custom genome or to index as a Built-in genome. Do you know of another public data provider?