BCALM Viewer

Generates a graph image with Graphviz DOT starting from a BCALM generated FASTA file representing a de Bruijn graph of sequencing data.

Usage

bcalm-viewer [OPTIONS] [INPUT] [DOT OPTIONS ...]

For more information: bcalm-viewer -h.

Workflow example

1. Generate the de Bruijn graph with BCALM:

bcalm -in list.fa -kmer-size 16 -max-memory 1000 -all-abundance-counts 

2. Generate the DOT file and the PDF final file:

bcalm-viewer -d pdf list.unitigs.fa

3. The resulting files are list.unitigs.gv and list.unitigs.gv.pdf.

Download builds

• Linux (64 bit)
• Linux (32 bit)
• macOS (64 bit)
• Windows (64 bit)

Requirements

To generate the final file (e.g. .pdf) graphviz dot is required. Without it the intermediate file (i.e. .gv) can still be generated.

The dot executable must be in system path; in alternative you can set the environment variable DOT_PATH.