S

    binchicken update

    Applies further processing to a previous Bin Chicken coassemble run. Note that all coassemblies can be run by rerunning the coassemble command unchanged except for adding --run-aviary.

    Any combinations of the following:

    • Generating unmapped reads files (--assemble-unmapped)
    • Running assembly/recovery for all/specific coassemblies through Aviary (--run-aviary, --coassemblies)
    • Downloading SRA reads (--sra)
    # Example: update previous run to run specific coassemblies
binchicken update --coassemble-output coassemble_dir --run-aviary \
    --coassemblies coassembly_0 ...

# Example: update previous run to perform unmapping
binchicken update --coassemble-output coassemble_dir --assemble-unmapped

# Example: update previous run to download SRA reads
# Note: requires sample names to be SRA IDs (e.g. SRA123456)
binchicken update --coassemble-output coassemble_dir --sra

# Example: update previous run to download SRA reads, perform unmapping and run specific coassemblies
binchicken update --coassemble-output coassemble_dir --sra \
    --assemble-unmapped \
    --run-aviary --coassemblies coassembly_0 ...

    OPTIONS

    INPUT ARGUMENTS

    --forward, --reads, --sequences FORWARD [FORWARD ...]

    input forward/unpaired nucleotide read sequence(s)

    --forward-list, --reads-list, --sequences-list FORWARD_LIST

    input forward/unpaired nucleotide read sequence(s) newline separated

    --reverse REVERSE [REVERSE ...]

    input reverse nucleotide read sequence(s)

    --reverse-list REVERSE_LIST

    input reverse nucleotide read sequence(s) newline separated

    --genomes GENOMES [GENOMES ...]

    Reference genomes for read mapping

    --genomes-list GENOMES_LIST

    Reference genomes for read mapping newline separated

    --coassembly-samples COASSEMBLY_SAMPLES [COASSEMBLY_SAMPLES ...]

    Restrict coassembly to these samples. Remaining samples will still be used for recovery [default: use all samples]

    --coassembly-samples-list COASSEMBLY_SAMPLES_LIST

    Restrict coassembly to these samples, newline separated. Remaining samples will still be used for recovery [default: use all samples]

    --sra

    Download reads from SRA (read argument still required). Also sets --run-qc.

    --download-limit DOWNLOAD_LIMIT

    Parallel download limit [default: 3]

    COASSEMBLY OPTIONS

    --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)

    --coassemblies COASSEMBLIES [COASSEMBLIES ...]

    Choose specific coassemblies from elusive clusters (e.g. coassembly_0)

    --coassemblies-list COASSEMBLIES_LIST

    Choose specific coassemblies from elusive clusters newline separated (e.g. coassembly_0)

    --assemble-unmapped

    Only assemble reads that do not map to reference genomes

    --run-qc

    Run Fastp QC on reads

    --unmapping-min-appraised UNMAPPING_MIN_APPRAISED

    Minimum fraction of sequences binned to justify unmapping [default: 0.1]

    --unmapping-max-identity UNMAPPING_MAX_IDENTITY

    Maximum sequence identity of mapped sequences kept for coassembly [default: 99%]

    --unmapping-max-alignment UNMAPPING_MAX_ALIGNMENT

    Maximum percent alignment of mapped sequences kept for coassembly [default: 99%]

    --run-aviary

    Run Aviary commands for all identified coassemblies (unless specific coassemblies are chosen with --coassemblies) [default: do not]

    --cluster-submission

    Flag that cluster submission will occur through `--snakemake-profile`. This sets the local threads of Aviary recover to 1, allowing parallel job submission [default: do not]

    --aviary-speed {fast,comprehensive}

    Run Aviary recover in 'fast' or 'comprehensive' mode. Fast mode skips slow binners and refinement steps. [default: fast]

    --assembly-strategy {dynamic,metaspades,megahit}

    Assembly strategy to use with Aviary. [default: dynamic; attempts metaspades and if fails, switches to megahit]

    --aviary-gtdbtk-db AVIARY_GTDBTK_DB

    Path to GTDB-Tk database directory for Aviary. Only required if --aviary-speed is set to comprehensive [default: use path from GTDBTK_DATA_PATH env variable]

    --aviary-checkm2-db AVIARY_CHECKM2_DB

    Path to CheckM2 database directory for Aviary. [default: use path from CHECKM2DB env variable]

    --aviary-assemble-cores AVIARY_ASSEMBLE_CORES

    Maximum number of cores for Aviary assemble to use. [default: 64]

    --aviary-assemble-memory AVIARY_ASSEMBLE_MEMORY

    Maximum amount of memory for Aviary assemble to use (Gigabytes). [default: 500]

    --aviary-recover-cores AVIARY_RECOVER_CORES

    Maximum number of cores for Aviary recover to use. [default: 32]

    --aviary-recover-memory AVIARY_RECOVER_MEMORY

    Maximum amount of memory for Aviary recover to use (Gigabytes). [default: 250]

    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

    update previous run to run specific coassemblies

    $ binchicken update --coassemble-output coassemble_dir --run-aviary --coassemblies coassembly_0 ...

    update previous run to perform unmapping

    $ binchicken update --coassemble-output coassemble_dir --assemble-unmapped

    update previous run to download SRA reads

    $ binchicken update --coassemble-output coassemble_dir --sra

    update previous run to download SRA reads, perform unmapping and run specific coassemblies

    $ binchicken update --coassemble-output coassemble_dir --sra --assemble-unmapped --run-aviary --coassemblies coassembly_0 ...

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