What is the poorest quality of data that RAST can handle?
• We recommend that your median contig length be at least 2 kbp; if your assembled sequence data are poorer quality that this, most of the contigs will not contain even one complete gene, and RAST will most likely abort with errors. We also recommend that your sequence data contain at most 1% ambiguity characters. It is possible that the metagenomic version of RAST, MG-RAST, may be able to do something with extremely low quality assemblies, since it is designed to handle large amounts of low-quality 454 data containing many frameshift errors. However, “Your Milage May Vary,” since MG-RAST is designed to analyze metagenomes rather than single genomes, and lacks many of the features of RAST.
Related Questions
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