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phylo42 / PEWO

Phylogenetic Placement Evaluation Workflows : Benchmark placement software and different reference trees
MIT License
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Simulation of reads with ART #8

Open matthiasblanke opened 3 years ago

matthiasblanke commented 3 years ago

Dear @blinard-BIOINFO , here is the code I used for injecting ART-simulated reads into PEWO; I think it would be nice to have such a feature in a future version of PEWO. Unfortunately, ART is not available as pip or conda package at the moment, so it has to be added manually to the PATH. Also my code is rather primitive for now, maybe you want to re-implement it in a more snakemakey-way... However, the accuracy results I am getting from this vary significantly from the current generation of reads (although number of errors and indels should be quite low) - I would appreciate if you could check whether I am doing something very basic wrong here. Best wishes, Matthias

blinard-BIOINFO commented 3 years ago

Hi, I saw that ART is is inconda: https://bioconda.github.io/recipes/art/README.html

We did not try it, but why did you say it's not in conda ? you used a different (incompatible?) version than the conda package ?

matthiasblanke commented 3 years ago

Apparently, I somehow missed that — even better then..