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DNA Sequencing pipeline for 454 GS/FLX runs

This is the pipeline process for 454 sequencing. I am not a biotech guy but after spending time, giving effort and getting help from my collague, I came up with a way to do that. The tools I used are NCBI SRA Toolkit and 454 sequencing tool for multiplexing. process Downloaded SRA files from … Converted these SRA files into SFF format using sff-dump tool $ sff-dump -A xxxx.sra Rebuilt the scores of converted sff dataset with sfffile tool $ sfffile -o xxxxxxn.sfff xxxxx.sff Split the file according to MID groupname $ sfffile -s ...

Linux Applications for another failure

Well, It is not a choice. I have to work on Linux platform since I joined a part time job at biotech gene annotation lab. Now,the website was settled and development is done. The researcher told me to analyze DNA sequence datasets and blah blah… So,Ubuntu becomes my home because most of bioinformatics tool are Linux binary applications. Let’s say around 6 months, this Linux distro fails me 3 times. Even though it said “Ubuntu 12.04 LTS(Long Term Support)”. You should call it as “Long Time to Stable”. Anyway,I have to use it and I try to find the best applications. Here is the list for nex...