Commit 0c1bec8c authored by ttreska57's avatar ttreska57
Browse files


parent 74270943
......@@ -132,14 +132,15 @@ First we have to combine all our contigs to one fasta-list
```shell /path/to/catalogue.fna.gz /path/to/assemblies/sample1/contigs.fasta
Second we use our aligned and sorted reads together with the fasta catalogue to generate the corresponding bins.
vamb --outdir path/to/outdir --fasta /path/to/catalogue.fna.gz --bamfiles /path/to/bam/*.bam -o C --minfasta 200000
Vamb is a metagenomic binner which feeds sequence composition information from a contig catalogue and co-abundance information from BAM files into a variational autoencoder and clusters the latent representation. It performs excellently with multiple samples, and pretty good on single-sample data. Vamb is implemented purely in Python (with a little bit of Cython) and can be used both from command line and from within a Python interpreter.
## Bin Refining
-DAS Tool
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