what’s the range of the expected sequencing error from seq.error? I’ve started using a commercial microbial community standard and I was wondering about what I should expect. So far a few orders of magnitude worse than what it’s shown in the MiSeq SOP…
Is make.contigs able to handle properly ‘very overlapping’ pairs? The sequencing centre does 2x250 for 16S-V4 and make.contigs seems to have problems. Using FLASH, modifying the defaults, clearly improves the amount of successfully assembled reads, the proportion of chimeras detected diminish (values around 50% with make.contigs vs around 10% with FLASH) and the sequencing error improves (not enormously but it does).
Not sure if it’s because of the full overlap of the reads or something else. Any idea?