After Novo assembly

Question

[lamlam]

After assembling (novo assembler ) a sequence of Tuberculosis I found that the number of base pair is greater than that number of base pair is the reference strain Is this logical?

[piet]

Is this logical?

Yes.

And computational biology is a quantitative science. Please tell us exactly how much greater your assembly is and which reference genome you have used.

[lamlam]

i used Mycobacterium tuberculosis H37Rv this reference has 4.4Mb and my sequence has 7.3 Mb?

[GenoMax]

Have you tried to compare the two to see how the assemblies are different? Use Mauve to compare.
Did you have an excess of sequence (> 100x gross coverage) that went into this assembly?

[piet]

Yes, you should map your contigs to the refseq and then identify contigs which do NOT map. Blast these contigs to identify their origin. Furthermore, your may plot GC-content of your contigs versus coverage. Do you see more than one cluster in the scatter plot?

Answer 1

[Ram]

There could be any number of reasons resulting in an increase in the number of bases - duplication at various levels, insertions, etc. Why is comparing base count any kind of metric?

[piet]

Why is comparing base count any kind of metric?

Tuberculosis genomes are extremely well conserved, much more than any other bacterial species.

[Ram]

Ah, I see. Thank you :)