Which spades subcommand to use for full synthetic promoters?

[biomystery]

I have a special case:

• We've made a library of synthetic promoters using a set of short motifs (~15bp average, n=20) by random ligation.
• The length of resultant synthetic promoters is within a range from 250bp~1000bp.
• In order to get longer promoter info, we did sonication and performed 2x300bp sequencing
• Now, we need to use the 2x300bp reads to recover the library of synthetic promoters (seqs + abundance)

Questions @asl :

• Can we apply Spade here? Is the assembly graph includes all possible promoter sequences in our library?
• Which sub-tools from Spade to use? Can we use biosyntheticSPAdes to annotate the promoter sequences?

Thank you so much!

[asl]

So, how long are your fragments overall?

[biomystery]

@asl The range should be 200~600bp post sonification. before sonication is 250~1000