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genovo

A docker image for running Genovo.

Metagenomic de novo Sequencing

Running

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.

Environment Variables

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
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dukegcb
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