Re: [galaxy-dev] building NGS indexes on user sequences

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