Development of a tool for NGS

Question

[ammarsabir15]

I am taking a course in perl. I have to submit a semester project in that course, I am thinking to develop a tool related to NGS data analysis, I have 3 months and language must be perl. For that I need suggestions.

Thanks,

[st.ph.n]

Combine what you've learned, and what you're interested in, and see what you think is feasible given your current skills. What could you do that would dazzle your instructor? Then, google. Google some more.

[WouterDeCoster]

You could write a script to make instructors not force students to use perl.

Answer 1

[Asaf]

Write a software that does a lot of small things on fasta or fastq files. Search here for questions like how can I change the header, how to extract etc. In the end you'll have a library that would be very useful. Since it's a course you should put the emphasis on building it correctly rather than doing awesome stuff.

[BioinfGuru]

I agree, this is the simplest thing to do.....definetly do this first...then if you have time... a more complicated thing to try would be to install NGS analysis tools that you call with your perl script....e.g. samtools, fastqc

Answer 2

[Devon Ryan]

Find a local lab that needs a pipeline written and write it in perl for them. That's certainly be doable in 3 months and would at least get used.

[ammarsabir15]

There is not such local labs in my country because bioinformatics is in infancy here. So this option is not much feasilble , secondly there is an option for collaboration, so may I write a new post for that ??

[Devon Ryan]

Sure, a collaboration would be good for you in many regards.