GraphBin2
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metagentools
☯️🧬 Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs
Hey, I have been trying to run Graphbin2 on a MetaFlye assembly but can't seem to get a successful run. Steps taken: 1) Assembly with metaflye 2) Use the 'gfa2fasta.py'...
With the current output, it is difficult to see what exactly was changed from the initial binning assignments, and if the binning assignments improved or not. I think it would...
Most initial binning tools output the contigs to different fasta files, one file per bin. Graphbin2 provides the new bin assignments, but does not re-output contigs based on the new...
Hi there, Im fairly new to running python scripts so apologies if I have missed something obvious. I have installed GraphBin2 by first downloading GraphBin2 v1.1, unzipping the file and...
Hi @Vini2 , Thanks for the great tool. More a conceptual question, your manuscripts all discuss binning of contigs, which seems to make sense to me (especially for paired-end Illumina...
Hi, Thanks for developing this tool. I met a problem when running the graphbin2. Below is my pipeline and the error i got: `flye --meta --nano-hq barcode05-trimmed-2000bp.fastq --genome-size 4.3m --out-dir...
Thanks for the great software! I'm wondering if it makes sense to weigh binning results with a confidence metric? A toy example I'm thinking of is: 3 contigs total, all...
graphbin2 doesn't seem to scale very well for large assemblies with large number of contigs. Given that a big fraction of the contigs generated by metaSPAdes are usually small, and...
The error: ``` GraphBin2 started ------------------- Total number of contigs available: 276680 Total number of edges in the assembly graph: 23569 Number of bins available in binning result: 13 Number...
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☯️🧬 Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs