Thursday, 3 November 2011

Available references for Ion Torrent Server download

There are reference files (plain fasta files zipped up) available on to use with your TS.

I would think it trivial for someone to write a shell script to curl / wget the reference and manually (or commandline ) create the reference index in the proper location.

But as of now, I can't find how to
1) manually create the reference index so that it shows in the realignment plugin as well.
2) reference files (there's only hg19 on the website)

2 isn't a big problem since the fasta requirements are simple enough.
no blank lines
no non IUPAC sequences

it's something u can include in the bash script with sed

Ok shall bother my PGM bioinfo FAS soon.

otherwise, I am stuck with the routine of downloading the sequences and zipping it and uploading on a win box (I do not have sliverlight on my Ubuntu)

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