binchicken evaluate

Evaluates the recovery of target genes by coassemblies suggested by above, finding the number of target genes present in the newly recovered genomes. Compares the recovery by phyla and by single-copy marker gene.

# Example: evaluate a completed coassembly
binchicken evaluate --coassemble-output coassemble_dir \
    --aviary-outputs coassembly_0_dir ...

# Example: evaluate a completed coassembly by providing genomes directly
binchicken evaluate --coassemble-output coassemble_dir \
    --new-genomes genome_1.fna ... --coassembly-run coassembly_0

Defaults to using genomes (from the provided coassemble outputs) with at least 70% complete and at most 10% contamination as estimated by CheckM2.

OPTIONS

BASE INPUT ARGUMENTS

--coassemble-output COASSEMBLE_OUTPUT

Output dir from coassemble subcommand

--coassemble-unbinned COASSEMBLE_UNBINNED

SingleM appraise unbinned output from Bin Chicken coassemble (alternative to --coassemble-output)

--coassemble-binned COASSEMBLE_BINNED

SingleM appraise binned output from Bin Chicken coassemble (alternative to --coassemble-output)

--coassemble-targets COASSEMBLE_TARGETS

Target sequences output from Bin Chicken coassemble (alternative to --coassemble-output)

--coassemble-elusive-edges COASSEMBLE_ELUSIVE_EDGES

Elusive edges output from Bin Chicken coassemble (alternative to --coassemble- output)

--coassemble-elusive-clusters COASSEMBLE_ELUSIVE_CLUSTERS

Elusive clusters output from Bin Chicken coassemble (alternative to --coassemble-output)

--coassemble-summary COASSEMBLE_SUMMARY

Summary output from Bin Chicken coassemble (alternative to --coassemble- output)

--aviary-outputs AVIARY_OUTPUTS [AVIARY_OUTPUTS ...]

Output dir from Aviary coassembly and recover commands produced by coassemble subcommand

--new-genomes NEW_GENOMES [NEW_GENOMES ...]

New genomes to evaluate (alternative to --aviary-outputs, also requires --coassembly-run)

--new-genomes-list NEW_GENOMES_LIST

New genomes to evaluate (alternative to --aviary-outputs, also requires --coassembly-run) newline separated

--coassembly-run COASSEMBLY_RUN

Name of coassembly run to produce new genomes (alternative to --aviary- outputs, also requires --new-genomes)

--singlem-metapackage SINGLEM_METAPACKAGE

SingleM metapackage for sequence searching

--prodigal-meta

Use prodigal "-p meta" argument (for testing)

EVALUATION OPTIONS

--checkm-version CHECKM_VERSION

CheckM version to use to quality cutoffs [default: 2]

--min-completeness MIN_COMPLETENESS

Include bins with at least this minimum completeness [default: 70]

--max-contamination MAX_CONTAMINATION

Include bins with at most this maximum contamination [default: 10]

CLUSTER OPTIONS

--cluster

Cluster new and original genomes and report number of new clusters

--cluster-ani CLUSTER_ANI

Cluster using this sequence identity [default: 86%]

--genomes GENOMES [GENOMES ...]

Original genomes used as references for coassemble subcommand

--genomes-list GENOMES_LIST

Original genomes used as references for coassemble subcommand newline separated

GENERAL OPTIONS

--output OUTPUT

Output directory [default: .]

--conda-prefix CONDA_PREFIX

Path to conda environment install location. [default: Use path from CONDA_ENV_PATH env variable]

--cores CORES

Maximum number of cores to use [default: 1]

--dryrun

dry run workflow

--snakemake-profile SNAKEMAKE_PROFILE

Snakemake profile (see https://snakemake.readthedocs.io/en/v7.32.3/executing/cli.html#profiles). Can be used to submit rules as jobs to cluster engine (see https://snakemake.readthedocs.io/en/v7.32.3/executing/cluster.html).

--local-cores LOCAL_CORES

Maximum number of cores to use on localrules when running in cluster mode [default: 1]

--cluster-retries CLUSTER_RETRIES

Number of times to retry a failed job when using cluster submission (see `--snakemake-profile`) [default: 3].

--snakemake-args SNAKEMAKE_ARGS

Additional commands to be supplied to snakemake in the form of a space- prefixed single string e.g. " --quiet"

--tmp-dir TMP_DIR

Path to temporary directory. [default: no default]

OTHER GENERAL OPTIONS

--debug

output debug information

--version

output version information and quit

--quiet

only output errors

--full-help

print longer help message

--full-help-roff

print longer help message in ROFF (manpage) format

EXAMPLES

evaluate a completed coassembly

$ binchicken evaluate --coassemble-output coassemble_dir --aviary-outputs coassembly_0_dir ...

evaluate a completed coassembly by providing genomes directly

$ binchicken evaluate --coassemble-output coassemble_dir --new-genomes genome_1.fna ... --coassembly-run coassembly_0