After the Novo assembler

[luc]

This looks better. What about the assembly size?
Adapter trimming, quality trimming, as well as error correction (optional) should happen before the assembly.
The A5 pipeline does all this for you be default.

Thank you
I use A5miseq i have 519 contig without trimming and for Spades 523 contigs.
i should do trimming after assembling or befor?

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Thank you
I use A5miseq i have 519 contig without trimming and for Spades 523 contigs.
i should do trimming after assembling or befor?

[luc]

This seem to be too many contigs for a bacterial genome, but I do not know anything about the Tuberculosis genome.

You could check the quality of your reads by aligning them to a reference.
Verify that you are not using too many reads for the assembly.
Did you do adapter trimming and quality trimming or error correction on your reads?

A5-miseq would include most of these steps in an easy pipeline:

https://sourceforge.net/projects/ngopt/

SPades is an easy to use assembler with a great error correction module:http://bioinf.spbau.ru/en/spades

(or if you want a really good assembly run a PacBio SMRT-cell)

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We sequenced the genome DNA only.
using Miseq and de novo assembly with Velvet tool.
number contig: 2045
I should normally have a number of pair of close base of the Reference!
What should I do?

[luc]

Not unexpected. How many contigs scaffolds did you get from what type of data from which assembler? Have you considered plasmids?

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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?