Question: Reference Guided De Novo assembly of Contigs generated from Illumina PE Reads
1
gravatar for WCG3
23 months ago by
WCG310
WCG310 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 • 1.7k views
ADD COMMENTlink modified 23 months ago by toralmanvar840 • written 23 months ago by WCG310
1
gravatar for toralmanvar
23 months ago by
toralmanvar840
toralmanvar840 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 23 months ago by toralmanvar840
0
gravatar for colindaven
23 months ago by
colindaven2.1k
Hannover Medical School
colindaven2.1k wrote:

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

ADD COMMENTlink written 23 months ago by colindaven2.1k
0
gravatar for jean.elbers
23 months ago by
jean.elbers1.3k
jean.elbers1.3k wrote:

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

ADD COMMENTlink written 23 months ago by jean.elbers1.3k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 817 users visited in the last hour