Package: binchicken
Bin chickenBin chicken - targeted recovery of low abundance metagenome assembled genomes through intelligent coassembly.Installation optionsInstall from BiocondaInstall latest release via bioconda.condacreate-nbinchicken-cbiocondabinchickenInstall from pipInstall latest release via pip.pipinstallbinchickenInstall from sourceCreate conda env frombinchicken.ymland install from source.gitclonehttps://github.com/AroneyS/binchicken.gitcdbinchicken
condaenvcreate-fbinchicken.yml
condaactivatebinchicken
pipinstall-e.Environment setupCreate subprocess conda environments and setup environment variables.
Conda prefix is the directory you want to contain the subprocess conda environments.
SingleM metapackage is the metapackage downloaded by SingleM usingsinglem data(seehttps://github.com/wwood/singlem).The latter databases are required only if you want to run Aviary directly using the--run-aviaryargument.
GTDB-Tk database is the directory containing the GTDB-Tk release (seehttps://github.com/Ecogenomics/GTDBTk).
CheckM2 database is the directory containing the CheckM2 database (seehttps://github.com/chklovski/CheckM2).
These can also be downloaded automatically by Aviary usingaviary configure --download gtdb singlem checkm2(seehttps://github.com/rhysnewell/aviary).binchickenbuild\--conda-prefix/path/to/conda/envs/dir\--singlem-metapackage/metapackage/dir\--gtdbtk-db/gtdb/release/dir\--checkm2-db/checkm2/db/dirAlternatively, set directory to contain subprocess conda environments and environment variables manually.
Subprocess conda environments will be created when required.condaenvconfigvarssetSNAKEMAKE_CONDA_PREFIX="/path/to/conda/envs"condaenvconfigvarssetCONDA_ENV_PATH="/path/to/conda/envs"condaenvconfigvarssetSINGLEM_METAPACKAGE_PATH="/metapackage/dir"condaenvconfigvarssetGTDBTK_DATA_PATH="/gtdb/release/dir"condaenvconfigvarssetCHECKM2DB="/checkm2/db/dir"Example workflow# Assemble and recover from each sample individually# 20 samples used for differential abundance binningbinchickencoassemble\--forward-listsamples_forward.txt--reverse-listsamples_reverse.txt\--run-aviary--single-assembly\--cores64--outputbinchicken_single_assembly# Assemble and recover from 2-sample coassemblies# Prioritising samples with genomes not previously recoveredbinchickeniterate\--coassemble-outputbinchicken_single_assembly\--run-aviary--assemble-unmapped\--cores64--outputbinchicken_2_coassembly# Perform another iteration of coassembly, with 3-samples this timebinchickeniterate\--coassembly-samples3\--coassemble-outputbinchicken_2_coassembly\--run-aviary--assemble-unmapped\--cores64--outputbinchicken_3_coassemblyBin chicken coassembleSnakemake pipeline to discover coassembly sample clusters based on co-occurrence of single-copy marker genes, excluding those genes present in reference genomes (e.g. previously recovered genomes).
The taxa of the considered sequences can be filtered to target a specific taxon (e.g. the phylum Planctomycetota).
Assembly and recovery can be run directly, or the coassemblies with differential-abudance-binning samples can be run in the tool of your choice.
Aviary assemble/recover commands are also generated based on proposed coassemblies.
Optionally, reads can be mapped to the matched bins with only unmapped reads being assembled.
Paired end reads of form reads_1.1.fq, reads_1_1.fq and reads_1_R1.fq are automatically detected and matched to their basename.# Example: cluster reads into proposed coassembliesbinchickencoassemble--forwardreads_1.1.fq...--reversereads_1.2.fq...# Example: cluster reads into proposed coassemblies based on unbinned sequencesbinchickencoassemble--forwardreads_1.1.fq...--reversereads_1.2.fq...--genomesgenome_1.fna...# Example: cluster reads into proposed coassemblies based on unbinned sequences and coassemble only unbinned readsbinchickencoassemble--forwardreads_1.1.fq...--reversereads_1.2.fq...--genomesgenome_1.fna...--assemble-unmapped# Example: cluster reads into proposed coassemblies based on unbinned sequences from a specific taxabinchickencoassemble--forwardreads_1.1.fq...--reversereads_1.2.fq...--genomesgenome_1.fna...--taxa-of-interest"p__Planctomycetota"# Example: find relevant samples for differential coverage binning (no coassembly)binchickencoassemble--forwardreads_1.1.fq...--reversereads_1.2.fq...--single-assembly# Example: run proposed coassemblies through aviary with cluster submission# Create snakemake profile at ~/.config/snakemake/qsub with cluster, cluster-status, cluster-cancel, etc.# See https://snakemake.readthedocs.io/en/stable/executing/cli.html#profilesbinchickencoassemble--forwardreads_1.1.fq...--reversereads_1.2.fq...--run-aviary\--snakemake-profileqsub--cluster-retries3--local-cores64--cores64Bin chicken evaluateEvaluates 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 coassemblybinchickenevaluate--coassemble-outputcoassemble_dir--aviary-outputscoassembly_0_dir...# Example: evaluate a completed coassembly by providing genomes directlybinchickenevaluate--coassemble-outputcoassemble_dir--new-genomesgenome_1.fna...--coassembly-runcoassembly_0Bin chicken iterateRun a further iteration of coassemble, including newly recovered bins.
Defaults to using genomes with at least 70% complete and at most 10% contamination CheckM2.
Automatically excludes previous coassemblies.# Example: rerun coassemble, adding new bins to databasebinchickeniterate--coassemble-outputcoassemble_dir# Example: rerun coassemble, adding new bins to database, providing genomes directlybinchickeniterate--coassemble-outputcoassemble_dir--new-genomesnew_genome_1.fnaBin chicken updateApplies further processing to a previous Bin chicken coassemble run: downloading SRA reads, generating unmapped reads files, and/or running assembly/recovery commands.# Example: update previous run to download SRA readsbinchickenupdate--coassemble-outputcoassemble_dir--sra--forwardSRA000001...--genomesgenome_1.fna...# Example: update previous run to perform unmappingbinchickenupdate--coassemble-outputcoassemble_dir--assemble-unmapped--forwardreads_1.1.fq...--reversereads_1.2.fq...--genomesgenome_1.fna...# Example: update previous run to run specific coassembliesbinchickenupdate--coassemble-outputcoassemble_dir--run-aviary--coassembliescoassembly_0...--forwardreads_1.1.fq...--reversereads_1.2.fq...--genomesgenome_1.fna...