direct mapping of color-space data against color-space

[begsch]

Hi,

I would like to know if someone has already tried to map color-space reads against other reads in color-space. The mapper of CoronaLite does not have an option for this - therefore I am at the moment analysing the source code for picking the necessary function (since at some point the reference genome has to be transfered in csfasta format and then further processed). Are there any other solutions for such an analysis?

I will keep you updated.

Regards,
begsch

[nilshomer]

Hi,

I would like to know if someone has already tried to map color-space reads against other reads in color-space. The mapper of CoronaLite does not have an option for this - therefore I am at the moment analysing the source code for picking the necessary function (since at some point the reference genome has to be transfered in csfasta format and then further processed). Are there any other solutions for such an analysis?

I will keep you updated.

Regards,
begsch

You can create a multi-fasta reference, where each "contig" is a read. Just translate the color-space reference into nucleotide space and run a color-space aware aligner (which will re-convert your reference into color space). Remember to retain the adaptor. Color space aligners include BFAST, BWA, MAQ, MOSAIK, SHRIMP, SOCS, ZOOM, ...

Nils