Genome assembly, removal of conting below 300 bp?
When assembling a genome with short read Illumina (or Illumia like) sequencing technologies is there an accepted bp size at which that contig should be removed from the final assembly? I have seen several papers use 300bp as a threshold. If a contig on 300 bp or smaller has good coverage I can’t see any benefits to removing it?
I am specifically working with fungal and bacterial assemblies, however I assume the logic can be applies across the board.
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