What I can do with fastq data of Illumina GE

[nhbach]

Hi everybody,

I am a doctor and very new in this area. We have intent to sequenced whole-genome of Mycobaterium tuberculosis with Illumina GAIIx from BaseClear: Paired-end reads 50 cycle 300 MB. And with fastq data, can I make short reads assembler to have full length of this genome?, detect SNP and mutation?

By using the CLC GW, we can do that?

Thank for any suggestions,


HB

[zee]

There are quite a few options to get to your goal. The first thing I would start doing is look for a close reference to map your reads and then assembly-by-reference.

I will give a very simple example of how you may want to proceed with command line software:

1) Find the reference genome e.g. mycobacterium TB strain X
2) Download all reference genome & plasmid sequences from Genbank
3) Download all reference annotations
4) Align all your reads to the reference genome using a good aligner e.g. novoalign, BWA, MAQ , SHRIMP. Ensure you output alignments in SAM format.
3) Convert your SAM format to BAM

Using the BAM file you can call SNPs and Indels with a variety of software packages, including SAMTOOLS itself.

Also, take a look at a software package called NESONI it's really good.

For GUI options I cant say much about CLC or these various others that would automate or get you some of the way or all of the way. You may also want to collaborate or contract somebody to do the work for you.

This is an academic forum but there are some vendors that could help you out. There will probably be more detailed answers than mine. IM me if you would like more specific help.

[maubp]

The CLCBio assembler works with Illumina paired end data, and if I recall correctly they do this for E. coli as an example. Depending on the repetitiveness of Mycobaterium tuberculosis it may be able to do a de novo assembly of this too. If not, strains of this have been sequenced before so a mapping or reference guided assembly could be done instead (using CLCBio or some other software).

[nhbach]

Thank you very much, your suggestions very helpful to me!

HB