Information and scripts for accessing genome sequence and annotation from various providers
- UCSC
- NCBI
- Ensembl
- JGI
See https://hgdownload.soe.ucsc.edu/goldenPath/currentGenomes/XXX/bigZips where
XXX is the genus and species of the organism. For example, XXX could be
Caenorhabidits_elegans. Within this directory, the soft-masked genome is
represented by chromFa.tar.gz. There is also a genes directory here, where
annotation from several sources is available. These files use the shortened
species and version, which for C. elegans is ce11 (that is eleven and not two
letter Ls). You can find the shortened name by retrieving the default index
listing from bigZips.
- fasta: hgdownload.cse.ucsc.edu/goldenPath/ce11/bigZips/chromFa.tar.gz .
- gtf: hgdownload.cse.ucsc.edu/goldenPath/ce11/bigZips/genes/*