Reference Genome Files

kubu4 edited this page Jun 6, 2014 · 9 revisions

Ensembl

In December 2013 Ensembl incorporated the data. Multiple files are available at Ensembl but here are a few key ones. Note they are updated regularly so check http://metazoa.ensembl.org/info/website/ftp/index.html to make sure you have the latest version. Direct FTP links to most current versions

QuickLinks to common files

Genome (soft-masked)
url

FASTA: http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa

Gzipped FASTA: http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa.gz

if mounted on eagle

/Volumes/web/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa

/Volumes/web/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa.gz


GigaDB

Genomic sequence was first made available July 12, 2012 at GigaDB

Fang, X; Li, L; Luo, R; Xu, F; Wang, X; Zhu, Y; Yang, L; Huang, Z (2012): Genomic data from the Pacific oyster (Crassostrea gigas). GigaScience. http://dx.doi.org/10.5524/100030

Data can be directly accessed from GigaDB, however a few of the key fasta files are linked below:


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