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I have a set of reads (I'm using fastq format but any format would do) and my program generates complete all-to-all coverage of the overlaps between those reads.
At this stage in development we'd love to see some output, so we want to feed this into something such as Tablet. However am I right in thinking that Tablet requires contig information to be supplied - it doesn't determine contigs itself from the overlap information if that is all it is given? (eg in {OVL ...} records)
Can anyone point me at a simple program that will take a series of reads and the overlap information, and output a list of contigs? I can massage formats to suit as long as there's no other information needed.
Failing that, a pointer to a good algorithm for OLC?
I do intend to write code to extract contigs myself eventually but if we can feed our overlap information into some existing pipleline we can start to use this new code in our work already.
Thanks,
Graham
At this stage in development we'd love to see some output, so we want to feed this into something such as Tablet. However am I right in thinking that Tablet requires contig information to be supplied - it doesn't determine contigs itself from the overlap information if that is all it is given? (eg in {OVL ...} records)
Can anyone point me at a simple program that will take a series of reads and the overlap information, and output a list of contigs? I can massage formats to suit as long as there's no other information needed.
Failing that, a pointer to a good algorithm for OLC?
I do intend to write code to extract contigs myself eventually but if we can feed our overlap information into some existing pipleline we can start to use this new code in our work already.
Thanks,
Graham