Hello everybody,
I am trying to improve my current assembly with some BAC sequences. I therefore thought of "scaffolding the scaffolds" and taking the BACs as an additional input data.
My data:
- 1800 scaffolds with an N50 of 3.6mb
- 50 BACs with a length of 120kb
I first wanted to use an assembler like Newbler or CARBOG, or a scaffolding program like Bambus or SSPACE, but they can't handle the input sizes or Ns in the data.
I also thought of using some BLAST version (maybe MEGABLAST) to map the BACs to the Scaffolds, but im not sure if this will work.
Has anyone any suggestions or hints?
Thank you very much!
Regards Björn
I am trying to improve my current assembly with some BAC sequences. I therefore thought of "scaffolding the scaffolds" and taking the BACs as an additional input data.
My data:
- 1800 scaffolds with an N50 of 3.6mb
- 50 BACs with a length of 120kb
I first wanted to use an assembler like Newbler or CARBOG, or a scaffolding program like Bambus or SSPACE, but they can't handle the input sizes or Ns in the data.
I also thought of using some BLAST version (maybe MEGABLAST) to map the BACs to the Scaffolds, but im not sure if this will work.
Has anyone any suggestions or hints?
Thank you very much!
Regards Björn
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