How can i analyze my NGS data?

[emmannaemeka]

Hi, I am new to bioinformatics. Recently, i got my sequence data for WGS using NGS Hiseq 2000. I don't know how to analyze the data. I spent considerable time using Fastqc, velvet 1.2.10 and mauve, but at the end i got a short base of about 140bases, the reference strain has 14mb sequence. I am wondering if the velvet cut the sequences or the raw data was bad.

Please how can i tell the quality of my reads? also, how can i determine the size of my reads?

[GenoMax]

Start by reading introductory chapters in this NGS wikibook. If you already have a reference sequence you don't need to use velvet (which is an assembler). What you instead need is an alignment program. What is the aim of the experiment you are doing?

[emmannaemeka]

Thanks for the reply. The organism i sequenced belongs to a different molecular type although the same species with the reference. It it thought that the molecular types represent different species. Therefore, I wish to compare my sequences data with the reference and secondly, this is the first sequence isolate for my country, I wish to make it a reference strain from my country

[GenoMax]

I would recommend starting with the alignment. Even if your strain is a different species it should still align well (90% or more) with the existing reference. The alignments will allow you to get an idea of how well the genome of your strain is represented in data you have. Later you could use the existing reference for reference assisted assembly, when you start working on that aspect.