Organize before Christmas

''The greater the difficulty, the more the glory in surmounting it, Epicurus''

This period I have to prepare a presentation for the other course of Applied Gene Technology, so I know that I will not have enough time to work on the project.

On 17th I am leaving back home to Greece for Christmas. I feel that it's gonna be hard to focus, but I 'll do my best!

We have agreed with Oliver and Taner that Oliver will do assembly with SOAP and me with Abyss. Oliver has already run Soap (SOAPdenovo2) with k=63 but as it seemed the N50 that he get is not good. It is around 120, which is very low.

In the meanwhile of this period I am looking on the documentation for Abyss in order to have a better feeling on what I am gonna do and don't just do random things.

• ABySS is an assembler based on de Bruijn graph
  • AByss is a good assembler for Illumina reads.
  • Abyss deals well with large genomes
  • Our input files for cpDNA reads are z4006c01.g.ipe.1.fq and z4006c01.g.ipe.2.fq. They are Illumina paired-end reads in a FastQ format, which is compatible with the required format of Abyss