Denovo genome assembly with multiple insert size libraries, both short and long reads

Question

[sunnykevin97]

Hi

Are there any denovo assemblers which assemble a genome in one go. By taking multiple insert-size libraries as input combinations of both short (Illumina) and long reads (Pacbio/Nanopore).

PacBio reads - 10Kb Illumina reads - PE 300 bp, 2.5 kb mate, 5 kb mate-pair and 9.3 kb mate-pair.

Suggestions encouraged.

Answer 1

[patrickdm]

Assuming you want to assembly a bacterial genome, you could give Unicycler a try:

Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. For the best possible assemblies, give it both Illumina reads and long reads, and it will conduct a short-read-first hybrid assembly.

Answer 2

[Mensur Dlakic]

Thank you for the encouragement.

SPAdes should be able to do what you want.

• https://github.com/ablab/spades (scroll down to "Supported data types")
• https://cab.spbu.ru/software/spades/