strainy
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katerinakazantseva
Graph-based assembly phasing
Hello! I'm trying to run stRainy on a collection of 14 related genomes to see if it will be useful to me in the future. i sequenced these 14 genomes...
In the output GFA file (strainy_final.gfa), some unitigs in L lines do not have corresponding S lines. This may be due to attempting to remove the unitigs at some point...
Hi I faced an error when I tried to make submodules/Flye ######################################################### z5438778@k250:~/stRainy $ make -C submodules/Flye make: Entering directory '/home/z5438778/stRainy/submodules/Flye' make -C /home/z5438778/stRainy/submodules/Flye/lib/minimap2 -j 4 make[1]: Entering directory '/home/z5438778/stRainy/submodules/Flye/lib/minimap2'...
Currently, the consensus dictionary stores the path to the .bed file. Instead of this, we can store the contents of the .bed file. This way the user can run the...
You might be able to squeak out a little performance boost by adding ` - pyston_lite_autoload` to environment.yml (using pyston 2.3.4 and python 3.8). Maybe give it a try for...
Create `setup.py` and make everything installable as a pip package. This is a first step to create a proper bioconda package.
`transform.py` currently is difficult to understand because there is so much code. Please split it into 2-3 modules based on function.
Don't use wildcard imports like `from metaphase.XX import *`. This makes the code difficult to read and prone to errors. Instead, either use `import metaphase.XX as YY`m and then use...