Thank you very much Dibakar Pal. You have been the first one to answer this question placed few years ago, so for that I say thank you.

I have already the staden package install in my computer with the program gap5 but my questions was more about a possible tutorial for gap5. I am not very computer wise and I was wondering if any other person had already made an alignment in gap5 with NGS data and if it would be possible to make a step by step tutorial or a progress report from having a fastq file to have it in gap5 to analyse it.

I have one of my Industrial Placement students looking at this problem, Mr Michael Garcia (Kingston University) and he found out the following link very interested:

http://avrilomics.blogspot.co.uk/2012/12/using-gap5-to-view-sambam-files.html#

*This are the steps that needs to be done to create a gap5 database with NGS files in the command line app:

          $ samtools index my.bam my.bam.bai

          $ samtools view my.bam > my.sam

          $ tg_index my.sam

The tg_index command will make files my.0.g5d and my.0.g5x, which are the Gap5 database files. To open Gap5 database you can select 'my.0.g5d’.

More information in the link provided.

My next questions would be: IGV vs UGENE vs gap5 which one is the best, advantage and disadvantages.

http://avrilomics.blogspot.co.uk/2012/12/using-gap5-to-view-sambam-files.html#