Convert SOLiD fastq to Illumina fastq

[Chipper]

Thanks, will BFAST work on a machine with <3 GBs of memory? (Mapping to whole mouse genome)

BWA should work with < 3Gb and is probably the best choice if resources are limited. Other programs that indexes reads rather than the genome will also work but won't be as fast (MAQ, ZOOM!, SOCS?).

[nilshomer]

Thanks, will BFAST work on a machine with <3 GBs of memory? (Mapping to whole mouse genome)

Mouse genome is ~3Gb right? In either case, you will have to split the reference to get it to fit on your machine. This is easy and supported with BFAST, although 3Gb is not very much RAM at all. How many reads, what length, and what computational resources do you have?

[samt]

Thanks, will BFAST work on a machine with <3 GBs of memory? (Mapping to whole mouse genome)

[nilshomer]

I want to do this in order to be able to use Bowtie software, but it doesn't support SOLiD data. Is there software to convert it?

If there was a conversion process, it would by definition support SOLiD data. It does not, so if you try to use it, even with double-encoded data, you will get poor results. Try BFAST or BWA for SOLiD data (you could also try SHRiMP).

[samt]

I want to do this in order to be able to use Bowtie software, but it doesn't support SOLiD data. Is there software to convert it?