where can I download the genome sequence of the Hawaii strain?

Model Organism: Worms Scientific Discussion
1

thanks very much.

2

They’re not completely helpful, but there’s this old thread, and this one.

3

there is an SNP sequence file in ws201 assembly, ftp://ftp.wormbase.org/pub/wormbase/releases/WS201/species/c_elegans/annotation/

However, in later assemblies, I didn’t find similar files.

4

A number of different projects have by now generated SNP calls for CB4856, and there is not universal agreement on what the Hawaiian strain sequence is!

WormBase has collated all the SNP calls for CB4856, and hundreds of other wild strains from a number of projects. In the near future, you will be able to use WormMine
to obtain a non-redundant list of variants for a strain of interest. In the meantime though, you can extract the information from our GFF files:

ftp://ftp.wormbase.org/pub/wormbase/releases/WS240/species/c_elegans/PRJNA13758/c_elegans.PRJNA13758.WS240.annotations.gff3.gz

Something like this will give you what you need:

cat c_elegans.PRJNA13758.WS240.annotations.gff3 | grep variation | grep polymorphism | grep CB4856

5

It may not be clear to everybody, since it was not announced prominently (apart from the WS250 release notes), but the hawaiian genome is available now via ftp
and can be browsed with gbrowse (jbrowse throws an error for me when I try to select “c_elegans_PRJNA275000” which is the hawaiian genome).
http://www.wormbase.org/tools/genome/gbrowse/c_elegans_PRJNA275000/
Directions: Go to the C. elegans species page and have a look at “Genome Assemblies”.
http://www.wormbase.org/species/c_elegans#03--10

Also have a look at the NCBI page for the hawaiian genome assembly:
http://www.ncbi.nlm.nih.gov/bioproject/PRJNA275000/

Cheers,
Mark