Question: How to extract genome from contigs
gravatar for tasmiaa.saleem02
9 weeks ago by
tasmiaa.saleem020 wrote:

I have a single end ion torrent hpv sample data. I have trimmed it with clc default parameters and done de novo assembly in clc workbench and I got these results N75 322, N50 408, N25 523, Minimum 200, Maximum 4,595, Average 394, Count 90,580 ,Total 35,717,540
Can anybody please guide me how to extract 8kb hpv genome from these contigs.

next-gen assembly genome • 97 views
ADD COMMENTlink modified 9 weeks ago by genomax83k • written 9 weeks ago by tasmiaa.saleem020

A search brought this page up which should be useful.

Sounds like you may have over-sequenced a small genome which always causes issues with assembly. You may want to normalize the data (if this is pure virus sequence) and re-try the assembly.

Aligning the consensus to the reference should give you an idea of the quality of assembly CLC produced.

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by genomax83k
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