SPAdes on raw reads produces more contiguous assembly than cleaned reads

[yeban]

N50 raw: 178 Kb; N50 cleaned (cutadapt -u 1 -q 12): 143 Kb

More contiguous doesn't necessarily mean more accurate, but it sure can look a bit awkward - what is the point of read cleaning then?

We may want to address this by increasing the coverage. Also, masking low-quality bases (seqtk seq -q 12 -n N) instead of trimming increases N50 to ~154 Kb. Contiguity further improves if orphaned reads are provided to SPAdes. Note also that SPAdes selects different k-mer sizes for raw and cleaned reads.