Im using this touorial to analyze and assembly mate pair NGS reads for my illumina reads : http://training.bioinformatics.ucdavis.edu/docs/2013/04/bootcamp/galaxy/genome-assembly.html#
Right now im almost at the last step: Comparing the Single and Paired End Assemblies. And there is a slight problem, because in the toutorial i should use:
"From NGS: QC and manipulation, run Count Fasta on each of the contig sets
- Start with default bin size (100) for each, but then maybe increase for PE assembly?
- Note the differences in number of sequences and in N50
- Which might be the “better” assembly?"
And after these procedure i should run lastz on my data (i've sucessfuly uploaded fasta data for my reference genome).
The problem is that in galaxy there is NO option "count fasta" :(, or at least on: http://galaxy.nbic.nl/
Could somebody tell me where i can find these tool?
Also maybe some of you have a better workflow to analyze mate pair read of Illumina to assembly the genome on basics of closed reference genome?
thank you very much for help. im very lost