Package: ibis-genome
IbisIbis (bin chicken) - targeted recovery of low abundance genomes through intelligent coassembly.Installation optionsInstall from sourceCreate conda env fromibis.ymland install from source.gitclonehttps://github.com/AroneyS/ibis.gitcdibis
condaenvcreate-fibis.yml
condaactivateibis
pipinstall-e.Create subprocess conda environmentsibisbuild--conda-prefix/path/to/conda/envsAlternatively, set directory to contain subprocess conda environmentscondaenvconfigvarssetSNAKEMAKE_CONDA_PREFIX="/path/to/conda/envs"Install from pipInstall latest release via pip.pipinstallibis-genomeIbis 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 coassembliesibiscoassemble--forwardreads_1.1.fq...--reversereads_1.2.fq...--no-genomes# Example: cluster reads into proposed coassemblies based on unbinned sequencesibiscoassemble--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 readsibiscoassemble--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 taxaibiscoassemble--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)ibiscoassemble--forwardreads_1.1.fq...--reversereads_1.2.fq...--single-assemblyIbis 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 coassemblyibisevaluate--coassemble-outputcoassemble_dir--aviary-outputscoassembly_0_dir...# Example: evaluate a completed coassembly by providing genomes directlyibisevaluate--coassemble-outputcoassemble_dir--new-genomesgenome_1.fna...--coassembly-runcoassembly_0Ibis iterateRun a further iteration of coassemble, including newly recovered bins.# Example: rerun coassemble, adding new bins to databaseibisiterate--aviary-outputscoassembly_0_dir...--forwardreads_1.1.fq...--reversereads_1.2.fq...--genomesgenome_1.fna...# Example: rerun coassemble, adding new bins to database, providing genomes directlyibisiterate--new-genomesnew_genome_1.fna...--forwardreads_1.1.fq...--reversereads_1.2.fq...--genomesgenome_1.fna...# Example: rerun coassemble, adding new bins to database, excluding previous coassembly combinationsibisiterate--exclude-coassembliesreads_1,reads_2--new-genomesnew_genome_1.fna...--forwardreads_1.1.fq...--reversereads_1.2.fq...--genomesgenome_1.fna...Ibis updateApplies further processing to a previous Ibis coassemble run: downloading SRA reads, generating unmapped reads files, and/or running assembly/recovery commands.# Example: update previous run to download SRA readsibisupdate--sra--coassemble-outputcoassemble_dir--forwardSRA000001...--genomesgenome_1.fna...# Example: update previous run to perform unmappingibisupdate--assemble-unmapped--coassemble-outputcoassemble_dir--forwardreads_1.1.fq...--reversereads_1.2.fq...--genomesgenome_1.fna...# Example: update previous run to run specific coassembliesibisupdate--run-aviary--coassembliescoassembly_0...--coassemble-outputcoassemble_dir--forwardreads_1.1.fq...--reversereads_1.2.fq...--genomesgenome_1.fna...