Kalanchoe: Difference between revisions
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= Data = | = Data = | ||
* ~5x 454 from a variety of library sizes | * ~5x 454 from a variety of library sizes | ||
* ~20x illumina. | * ~20x illumina. | ||
* Location: | |||
/fs/szattic-asmg7/Kalenchoe_genome/ | |||
= Assembly = | = Assembly = | ||
| Line 12: | Line 16: | ||
SOAP uses a de bruijn graph data structure that is well suited for short illumina reads but it is not enough flexible in order to handle 454 reads. | SOAP uses a de bruijn graph data structure that is well suited for short illumina reads but it is not enough flexible in order to handle 454 reads. | ||
Newbler, instead, is based on Overlap Layout Approach that work well with long reads | Newbler, instead, is based on Overlap Layout Approach that work well with long reads | ||
* CABOG ... throws a lot of errors on our architecture for some reason | |||
Revision as of 05:55, 9 February 2011
Data
- ~5x 454 from a variety of library sizes
- ~20x illumina.
- Location:
/fs/szattic-asmg7/Kalenchoe_genome/
Assembly
Blogs
assemble the illumina lane with SOAPdenovo and then assemble with newbler the 454 lanes and the resulting contig of SOAP2. SOAP uses a de bruijn graph data structure that is well suited for short illumina reads but it is not enough flexible in order to handle 454 reads. Newbler, instead, is based on Overlap Layout Approach that work well with long reads
- CABOG ... throws a lot of errors on our architecture for some reason