mapping against multiple reference sequences

[ssharma]

Hi All,
Is there any alignment/mapping tool that can map reads to multiple reference sequences (database of sequences)?

Thanks
Ssharma

[GenoMax]

Can you provide some additional specifics? All aligners can align against a set of sequences (converted to an appropriate index). This set could potentially have more than one genome/build in it.

[ssharma]

Thanks a lot GenoMax for your quick reply.
I have few million illumina reads and i want to map/align them to a database that contains few million reads (actually they are some specific reads from nt database).

Thanks

[GenoMax]

All you should need is a multi-fasta format file of nt reference sequences. Create the necessary indexes (using the aligner you are planning to use).

[ssharma]

Thanks GenoMax,