Drosophila reference genomes

Question

[ATCG]

Which Drosophila genome data( reference genome and annotation files) do most scientists use? Thanks!

[wm]

We mostly use the reference from UCSC (dm6, BDGP6), and annotations from flybase: http://flybase.org

[wm]

here is the reference data for fruitfly on UCSC, And I used to batch download genomes from UCSC, there is rsync service, easy to maintain the local dataset.

see here: http://hgdownload.soe.ucsc.edu/downloads.html#fruitfly

$ rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/dm6/bigZips/ .

Answer 1

[GenoMax]

NCBI/Ensembl/UCSC have Fly genome versions available.

You are also going to find Fly genomes at FlyBase (parts may need a subscription).

[ATCG]

Okay thanks. Is there a more specific link? I downloaded genome files (~23) from http://www.fruitfly.org but it's difficult to know which is the complete genome reference ( similar to hg19.fasta). Thanks!

[GenoMax]

I will use example of Ensembl but same thing for other two sites.

Genome sequence.
Annotation

[ATCG]

What about the transcriptome? For example, to align to the reference genome I would use the genome.fa and features.fa but If I want o to align to the transcriptome I would need a transcripts.fa Thank you so much for your help!

[GenoMax]

cDNA files are here at Ensembl or these are the super-set of all transcripts coding sequences resulting from Ensembl gene predictions.

NCBI has fly transcripts here.

[ATCG]

Probably the most comprehensive site I found: https://www.ncbi.nlm.nih.gov/assembly/GCF_000001215.4/