What clusters end up in gene accessory_binary_genes.fa ?

[tseemann]

The manual says:

First of all we construct a FASTA file with the binary presence and absence of genes, where 'A' means a gene is present and 'C' means it is absent. Only the first 4000 genes in the accessory genome are considered

Based on some data we have tried, it seems that singleton clusters do NOT end up in the file?

eg. 10 samples, mostly clonal, but 1 with a plasmid, causes tree to be mostly flat, no sites in the .fa file for the plasmid genes.

[tseemann]

I've found this code: https://github.com/sanger-pathogens/Roary/blob/056512409fcb0e817cf16ae554792816b80b9356/lib/Bio/Roary/AccessoryBinaryFasta.pm

And it seems besides the 4000 gene limit, there is some 5% upper and lower bound, which i assume trims clusters that have membership numbers too low or too high?

Is there a way to script / parameter this from the command line tools?

[andrewjpage]

Hi Torsten,

I wanted to cap the size of the file sent into FastTree since it can be
memory hungry. Running a few tests, I think I may have been a bit too
cautious here. My original thinking was to focus on getting the general
high level groupings in a reasonable order (hence getting rid of the top
and bottom 5%). I'll remove this restriction and see how things go.
Andrew

On 20 January 2016 at 01:56, Torsten Seemann notifications@github.com
wrote:

I've found this code:
https://github.com/sanger-pathogens/Roary/blob/056512409fcb0e817cf16ae554792816b80b9356/lib/Bio/Roary/AccessoryBinaryFasta.pm

And it seems besides the 4000 gene limit, there is some 5% upper and lower
bound, which i assume trims clusters that have membership numbers too low
or too high?

Is there a way to script / parameter this from the command line tools?

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[tseemann]

Thanks!
Nullarbor now produces pan-genome trees and they seem to have more resolution now.

[jacorvar]

Hi @andrewjpage ,

is it already possible to get the accessory_binary_genes.fa from the gene_presence_absence.csv file using any script from the command line?

Thanks