Monday, 11 October 2010

pitfalls for SAET for de novo assembly

Spotted in manual for

SOLiD™ System de novo Accessory Tools 2.0

Usage of pre-assembly error correction: This is an optional tool which was
demonstrated to increase contigs length in de novo assembly by factor of 2 to 3. Do not use this tool if coverage is less than 20x. Overcorrection and under-correction are equally bad for de novo assembly; therefore use balanced number of local and global rounds of error correction. For example, the pipeline will use 1 global and 3 local rounds if reads are 25bp long, and 2 global and 5 local rounds if reads are 50bp long.

Is it just me? I would think it is trivial to implement the correction tool to correct only when the coverage is > 20x. Not sure why you would need human intervention.

No comments:

Post a Comment

Datanami, Woe be me