Question: Reference Guided De Novo assembly of Contigs generated from Illumina PE Reads
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gravatar for wayne.gatlin3
3 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 • 237 views
ADD COMMENTlink modified 3 months ago by toralmanvar420 • written 3 months ago by wayne.gatlin30
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gravatar for colindaven
3 months ago by
colindaven740
Hannover Medical School
colindaven740 wrote:

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

ADD COMMENTlink written 3 months ago by colindaven740
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gravatar for jean.elbers
3 months ago by
jean.elbers290
jean.elbers290 wrote:

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

ADD COMMENTlink written 3 months ago by jean.elbers290
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gravatar for toralmanvar
3 months ago by
toralmanvar420
toralmanvar420 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 3 months ago by toralmanvar420
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