Make a complete genome sequences from Illumina data

[nhbach]

Dear all,
I have a raw data of re-sequencing of M. tuberculosis' genome. We run on GAIIx system with paired end (50 bp sequence run).

I try to assembly with Velvet programs with default kmer=31. We obtain config files with 2344 nodes (open with Genious program), we ligate all contigs by order and have a concatenated sequence with 4.559.459 bp.

This is the first time I work with this field, so I'm wondering this is a right process to have complete genome sequences? How to check SNP from this sequences?...

Thank for any suggestion!

[colindaven]

It might be better to do a reference assembly of your reads versus the genome as opposed to the de novo assembly you've done.

Try Stampy, or bwa for alignment.

Then use Samtools or GATK to get SNPs from the alignment.

If you want to stick to your de novo contigs just try blasting them against the nearest sequenced neighbour.

[nhbach]

Thanks for your suggestion!