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2.5 years ago
Kumar
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170
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!
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.
With Illumina reads the best version of the assembly is the one you get form the assembler
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.
You can try Unicycler
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.
Hi Kumar,
You should create a new post.
I did (How to make hybrid assembly of a viral genome), if you have an idea, please let me know.
Thank you!