A docker image for running Genovo.
Metagenomic de novo Sequencing
The Docker image built by the Dockerfile is designed to be used by docker-pipeline.
Genovo binaries are installed in /opt. The image's default command, genovo.sh, is modeled after run_genovo.py from YoderLab/MMAP.
| Variable | Description | Type | Required? | Default |
|---|---|---|---|---|
| CONT_INPUT_READS_FILE | FASTA file containing reads to assemble | Input | Yes | |
| CONT_OUTPUT_CONTIGS_FILE | Results file, to contain contigs | Output | Yes | |
| CONT_INPUT_ASSEMBLE_ITERATIONS | The number of iterations to run when assembling | Parameter | No | 10 |
| CONT_INPUT_FINALIZE_CUTOFF | The minimum length to use when outputting assembled contig | Parameter | No | 250 |
docker pull dukegcb/genovo