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

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.

gene genome
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updated by Mensur Dlakic Mensur Dlakic • written by sunnykevin97 sunnykevin97

2 answers

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.

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written by patrickdm • patrickdm

Thank you for the encouragement.

SPAdes should be able to do what you want.

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written by Mensur Dlakic Mensur Dlakic

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