Question: Reference Guided De Novo assembly of Contigs generated from Illumina PE Reads
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gravatar for wayne.gatlin3
11 months ago by
wayne.gatlin30 wrote:

Hello,

I'm trying to do a de novo assembly of a mycobacterial isolate that is likely similar to one of several published complete genomes on NCBI that I am hoping to use as a reference. I was able to use SPAdes to assemble contigs from Illumina PE reads, but now I have a few thousand contigs that need to be arranged. Anyone have suggestions for (preferably Galaxy or open source) tools to align contigs to a published similar species reference? I wish I had some long reads, but alas, I do not.

Thanks!

Wayne

alignment assembly • 787 views
ADD COMMENTlink modified 11 months ago by toralmanvar750 • written 11 months ago by wayne.gatlin30
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gravatar for colindaven
11 months ago by
colindaven1.1k
Hannover Medical School
colindaven1.1k wrote:

Medusa may work https://github.com/combogenomics/medusa

ADD COMMENTlink written 11 months ago by colindaven1.1k
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gravatar for jean.elbers
11 months ago by
jean.elbers720
jean.elbers720 wrote:

Ragout (https://github.com/fenderglass/Ragout) is also another option.

ADD COMMENTlink written 11 months ago by jean.elbers720
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gravatar for toralmanvar
11 months ago by
toralmanvar750
toralmanvar750 wrote:

You can use nucmer program of MUMmer package for aligning your denovo assembly to reference genome and can upload its output file (.delta) to assemblytics. It will give you interactive dot plot (by arranging denovo assembled scaffolds on reference genome) as well as helps in analyzing variants between two genomes aligned.

ADD COMMENTlink written 11 months ago by toralmanvar750
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