Case 1: Cleanup of transcriptomic reads based on full-length, normalized cDNA protocol (Roche 454 Titanium, 1.2M reads), co-assembly with Illumina reads (239M reads, 100bp), initial analysis of the contigs/exons and ORFs.
“I am very impressed. You seem to have generated a quite compacted, non-redundant set of contigs that seem to make sense; their total number seems what one might expect, their length is plausible and their match to *** is what one might anticipate. Very well done!”
Prof. Dr. Robert J. Paxton, LMU Halle, Germany
Case 2: Cleanup of bacterial whole-genome shotgun data, re-assessment of high-qual and low-qual basecalls (Roche software underestimates PHRED qualities in some cases), produced improved assembly over past attempts while scaffold count dropped to about 1/5.