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kmer-ord bin

Launch the interactive binning interface (b2w) for manual exploration and binning. b2w is built using Dash.

  • exploring embeddings interactively
  • selecting reads using lasso tools
  • creating bins
  • exporting bins (both sequences and metadata)

Usage

kmer-ord bin [OPTIONS]

Input / Output

Parameter Flag Type Default Description
Database path -d, --db path — SQLite/SpatiaLite database
Output directory -o, --output path bins Directory where bins are written

Server configuration

Parameter Flag Type Default Description
Host --host str 127.0.0.1 Address to bind the web server
Port --port int 8050 Port for the web application

Example

kmer-ord bin \
  -d results/kmerord.sqlite \
  -o results/bins

then open in browser:

http://127.0.0.1:8050

What happens

  • A local Dash server is started
  • Serves the interactive interface in a browser
  • Loads embeddings and features from the database

Output

Exported bins are written to:

<output_dir>/

Following files are generated for each bin:

  • <bin_name>.csv - table of selected reads and features
  • <bin_name>.fasta or .fastq - sequences

See also: