Off topic:Genome Analysis

Question

[Zak]

Hello friends

I am looking for some sort of protocol for genome analysis ,starting with assembly of contigs.

I have a nucleotide sequencing data some fungal species and now I'm interested in performing a genome analysis of the data, I have a prior knowledge of protein analysis but I have never performed a genome analysis,

I have read about genome analysis but there doesn't seem to be a proper methodology to it except

1. Assembly of genomic sequence
2. Predicting repeated sequences
3. Gene Prediction
4. EST and CDNA Sequences analysis
5. GENOME ANNOTATION

Is there some how I can get some reference in this topic