In particular I was thinking of the read-mappers like Bowtie & BWA. The indexes are made by the sysadmin and added to the .loc file 'by hand'. It would be good if a user could add their sequence of interest as a library - maybe a new genome, or refererence sequence like mitochondria or something - and then create the required index themself, then they can run their read mapping on that sequence. Cheers, Mike. On Wed, Dec 1, 2010 at 1:01 AM, Peter <peter@maubp.freeserve.co.uk> wrote:
On Tue, Nov 30, 2010 at 2:14 PM, Michael Pheasant <mike@pheasant.co.nz> wrote:
Hi
We want to allow users to index sequences in galaxy (for example in the data libraries) for use with NGS tools (Bowtie, BWA, etc). Has anyone made tools for NGS indexing?
Hi Mike,
Could you clarify what you mean by NGS indexing? There are lots of different index schemes - e.g. *.BAI are indexes for BAM files, similarly samtools has its own index scheme for FASTA files. Other examples include BioPerl flat file indexes (including OBDA text file and BSD indices) for sequential files (e.g. FASTA, GenBank, EMBL, ...).
Peter