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VIB-PSB / i-ADHoRe

i-ADHoRe is a highly sensitive software tool to detect degenerated homology relations within and between different genomes.
GNU Affero General Public License v3.0
14 stars 4 forks source link

Is there documentation? #13

Closed taprs closed 9 months ago

taprs commented 9 months ago

Dear i-AdHoRe 3.0 team,

Your software seems to do great job, and quickly! At least inasmuch as I can tell from using it within the wgd v2 pipeline. Thank you for making it!

However, as I tried to make more use of its output, I faced lack of explanations of what some fields in the output mean. I tried to find more help on the website referenced in README, but it only points to the paper with details about the algorithm. My attempts to invoke a help message in the command line were also unsuccessful.

My question is: Is there a resource that would explain the meaning of all output files & fields therein as well as the design of the config file?

If directly helping me with my usecase would be easier: I want to break my genome assembly into longest collinear blocks (i.e. getting two fragments of an assembly for every non-overlapping longest self-collinearity hit). By this I am trying to get the "subgenomes" of an ancient polyploid which has experienced a few homoeologous recombination events for further phasing.

taprs commented 9 months ago

Ah, spotted the documentation folder — would be cool to reference the manual in README along with the paper! Closing the issue now.