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Vini2
🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
**Describe the bug** I am trying to use phables on my metagenome assembly, assembled with metaFlye. **To Reproduce** Steps to reproduce the behaviour, including the 1. Command executed ``` phables...
Hi, I am running into an error with scan_smg because it says that my edges.fasta.frag.faa file is empty. I am not sure why this is the case as my input...
Hi, I'm new to this field, I was recently reading an article called "Phables: from fragmented assemblies to high quality bacteriophage genomes" and I wanted to reproduce some of the...
Replace MFD-ILP code written using gurobi with an open source solver such as [lpsolve](https://lpsolve.sourceforge.net/5.5/Python.htm) or [pyglpk](https://pyglpk.readthedocs.io/en/latest/).
Hey, the temporary/partial bam files are created in the directory where I run phables rather than in the output directory. Do you think it is possible to enhance that? `*0001.bam`,...
**Is your feature request related to a problem? Please describe.** Currently, phables takes assembly graph files only in `gfa` format. **Describe the solution you'd like** Add a converting step if...
**Is your feature request related to a problem? Please describe.** Currently, one cannot view the assembly graph of a single component without loading the entire assembly into a program such...
**Is your feature request related to a problem? Please describe.** The current version does not provide which unitigs make up each component. **Describe the solution you'd like** Provide information on...
Hey, Thanks for developing Phabels. I've installed Phables in conda (mamba) environment, and getting this error in each run including the test (which somehow worked correctly at first). Do you...
When using long reads (and not fully reading the manual) you may forget to add the `--longreads` flag. Phables doesn't work well on long reads without that flag, but is...
