About assembly files

[aloliveira]

I wanted to know what are the assembly files most commonly used for NexGen sequencing? I am familiar with the file afg, and ace (typical for sanger).

The ace file is well documented but i can not find the documentation of afg file. Does anyone know where I can get it?

I wonder if there are parsers (PERL language) available for both the ace and for afg? (to extract reads that make up the contig, the contig size, quality of reads, etc.)

Best regards,
André

[flxlex]

The agp file format is descirbed here:

http://www.ncbi.nlm.nih.gov/projects/genome/assembly/agp/AGP_Specification.shtml

I think there are bioperl modules that can parse the ace file...

[A_Morozov]

There definitely are. http://www.bioperl.org/wiki/Module:B...mbly::Scaffold and http://www.bioperl.org/wiki/Module:Bio::Assembly::IO Though you'll have some speed issues if you want to parse your 5 Gb of reads via perl.