Vijini Mallawaarachchi
Vijini Mallawaarachchi
Add args.paths validation for Flye input to check that `assembly_info.txt` is provided.
Use nox for the testing suit
Integrate coverage information from co-assemblies to make use of differential coverage across multiple samples.
Use distributed computing to distribute and bin multiple metagenomes. Sample MPI code: [https://github.com/Vini2/distribin](https://github.com/Vini2/distribin). Use Cogent3's parallel computing capabilities [https://cogent3.org/doc/examples/parallel.html](https://cogent3.org/doc/examples/parallel.html).
Add support to input depth file from MetaBAT2's `jgi_summarize_bam_contig_depths`.
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/).
**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...
Hello Cobra authors! Thanks for building this tool. I keep getting this error of a contig file not being created. ``` Traceback (most recent call last): File "/home/mall0133/miniconda3/envs/cobra/bin/cobra-meta", line 10,...