Assemly: MetaSPAdes hybrid: scaffolds vs contigs
Use scaffolds.fasta
instead of contigs.fasta
for hybrid assembly
For SR, using contigs makes more sense.
For hybrid assemblies, using scaffolds.fasta
should be a better choice.
Also, using scaffolds.fasta
is recommended: SPAdes manual v3.14.1
<output_dir>/scaffolds.fasta contains resulting scaffolds (recommended for use as resulting sequences)
<output_dir>/contigs.fasta contains resulting contigs