Exercises

[Teunis]

Dear,
I have been exercising in bioinformatics on the Rosalind web site
The problems learned me a lot.
The last problem I solved was assembling a circular (bacterial) genome.
The input were about 600 reads of 50 bp. The correct answer I obtained (in 20 sec, cheap computer) was a sequence of about 2000 bp. I program with the language PASCAL because it gives me a lot of freedom to construct my own data structure.
The problem is that I can't get another (bigger) dataset to give my algoritm a try.
Is someone willing to give me a dataset of reads and verify my answer?
Reads of circular DNA or contigs of DNA from eukaryotic cells are welcome.
The reads can be of mixed lengths and (almost) perfect.
Please, let me know if I can expect an answer in the SEQanswer community.
Thanks for reading

[Brian Bushnell]

Teunis,

You can certainly download reference genomes from ncbi:

ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/

The files you want will end with "fna". They are mostly 2.5 to 5 million bp. If you want something smaller, you can just open them with a text editor and just keep the first 1000 lines or so. Then you can use a tool like randomreads.sh (packaged with BBTools) to generate random reads of whatever quality, quantity, or length you want.

In Linux, the command would be something like this:

randomreads.sh ref=ecoli.fna out=reads.fq reads=100000 length=600 maxq=40 midq=35 minq=30

You can verify your answer with a program called "Quast".

[Teunis]

Thanks I will give it a try. Bye Bye