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!
Drosophila reference genomes
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I will use example of Ensembl but same thing for other two sites.
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.
Probably the most comprehensive site I found: https://www.ncbi.nlm.nih.gov/assembly/GCF_000001215.4/
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We mostly use the reference from UCSC (dm6, BDGP6), and annotations from flybase: http://flybase.org
here is the reference data for fruitfly on UCSC, And I used to batch download genomes from UCSC, there is
rsyncservice, easy to maintain the local dataset.see here: http://hgdownload.soe.ucsc.edu/downloads.html#fruitfly