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How to assemble a genome from scaffolds to Chromosome level

Hi, I have got bacterial fastq files and I assembled these files in scaffolds using SPAdes. I am looking to assemble these scaffolds at the Chromosome level. Please let me know if there is any pipeline/software to do this. I tried to use ABACAS but I'm not sure if it is the correct way. I would appreciate any suggestions. Thank you!

genome assemble scaffolds
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written by Kumar Kumar

To get a chromosome level assembly, you will need sequencing reads from different technologies: Illumina reads + long-reads, or long-reads only. I would never use tools such ABACAS unless I am 100% sure that both genomes are identical. Bacterial strains belonging to the same species can be quite different.

I would appreciate any suggestions.

With Illumina reads the best version of the assembly is the one you get form the assembler

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written by andres.firrincieli andres.firrincieli

Thank you for your suggestion. We are planning to run MinION for long reads. Can you please let me know which process I should use to assemble long reads (MinION) output to Chromosome level.

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written by Kumar Kumar

Hi, could you please let me know any pipeline for viral genome assembly. I have got pair-end reads from Illumina and long read from MinION and I am looking for Hybrid assembly of a viral genome. I tried Unicycler but it is for bacterial genome assembly.

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written by Kumar Kumar

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