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After Novo assembly

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?

assembly
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updated by GenoMax GenoMax • written by lamlam • lamlam

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.

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written by piet piet

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

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written by lamlam • lamlam

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?

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written by GenoMax GenoMax

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?

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written by piet piet

1 answer

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?

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written by Ram Ram

Why is comparing base count any kind of metric?

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

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written by piet piet

Ah, I see. Thank you :)

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written by Ram Ram

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