How can I do a Hybrid Assembly of Long and Short Reads?
Go Back It is possible to do a hybrid assembly of long reads, e.g. PacBio or Oxford nanopore, and short reads, e.g. Illumina, in two different ways using QIAGEN CLC software.
A small benchmark shown below, shows that option 1 is in general the better approach. However, if option 1 does not give good results on your data we recommend trying option 2 instead.
Benchmark comparing options for hybrid assembly using QIAGEN CLC software: AP = Alignment percentage ANI = Average Nucleotide Identity Note: Join Contigs tool cannot use reads longer than 99,999 base pairs
On the images below you can find example workflow for the two options: Option 1: De Novo Assemble Long Reads and Polish with Reads Workflow |