I'm assembling a genomic region about 10Mb, using data from various platforms. Here are the types of data I have:
1. Some Sanger sequences of BAC ends and target genes
2. Single end 454 reads
3. Single end 50 bp Solexa reads
4. Paired end 74 bp Solexa reads
I think my current strategy is to assemble those data separately into 4 pools of contigs. Then I would like to assemble the 4 pools of contigs and then scaffold them together (with the PE Solexa data). There are two strategies:
A. Assemble those contigs first (with CAP3 or so), and use the Solexa PE reads to help scaffolding the final long contigs.
B. Assemble the contigs together with all the Solexa PE reads, in software like MIRA, then the scaffolding process is automatically done within MIRA.
Do people have an idea which one is better? For strategy A to work, I assume I would need to map the Solexa PE reads to the contigs (with software like BWA) and use the mapping information for scaffolding. Do people know of a scaffolding software that could deal with this?
Thanks,
Cheng-Ruei Lee
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