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Posts by anton
... Please note that in order to use SPAdes 3.1+ for mate-pair only assemblies you need to have the so-called "high quality mate pairs". Right now such mate pairs can only be generated using Nextera mate pair protocol. Everything else would give you suboptimal assemblies. ...
Answer: A: scaffolds and contigs SPADES
... It's perfectly ok that scaffolds coincide with contigs in case of single paired-end library - the assembler may simply resolve almost all short repeats and thus there is nothing to scaffold. ...
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