ibis-genome 0.8.0

Ibis (Australian bin chicken) - targeted recovery of low abundance genomes through intelligent coassembly

Ibis

Ibis (bin chicken) - targeted recovery of low abundance genomes through intelligent coassembly.

Installation options

Install from pip

Install latest release via pip.

pip install ibis-genome

Install from source

Create conda env from ibis.yml and install from source.

git clone https://github.com/AroneyS/ibis.git
cd ibis
conda env create -f ibis.yml
conda activate ibis
pip install -e .

Ibis coassemble

Snakemake 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). Creates graph with samples as nodes and the number of overlapping sequences provided by SingleM. The taxa of the considered sequences can be filtered to target a specific taxon (e.g. the phylum Planctomycetota). The graph is clustered using the Girvan-Newman algorithm to provide sample groupings. Aviary assemble/recover commands are generated based on proposed coassemblies. Optionally, reads can be mapped to the matched bins with only unmapped reads being assembled.

# Example: cluster reads into proposed coassemblies
ibis coassemble --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --no-genomes

# Example: cluster reads into proposed coassemblies based on unbinned sequences
ibis coassemble --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --genomes genome_1.fna ...

# Example: cluster reads into proposed coassemblies based on unbinned sequences and coassemble only unbinned reads
ibis coassemble --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --genomes genome_1.fna ... --assemble-unmapped

# Example: cluster reads into proposed coassemblies based on unbinned sequences from a specific taxa
ibis coassemble --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --genomes genome_1.fna ... --taxa-of-interest "p__Planctomycetota"

# Example: find relevant samples for differential coverage binning (no coassembly)
ibis coassemble --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --single-assembly

Ibis 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
ibis evaluate --coassemble-output coassemble_dir --aviary-outputs coassembly_0_dir ...

Ibis iterate

Run a further iteration of coassemble, including newly recovered bins.

# Example: rerun coassemble, adding new bins to database
ibis iterate --aviary-outputs coassembly_0_dir ... --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --genomes genome_1.fna ...

Ibis update

Applies further processing to a previous Ibis coassemble run: downloading SRA reads, generating unmapped reads files, and/or running Aviary commands.

# Example: update previous run to download SRA reads
ibis update --sra --coassemble-output coassemble_dir --forward SRA000001 ... --reverse SRA000001 ... --genomes genome_1.fna ...

# Example: update previous run to perform unmapping
ibis update --assemble-unmapped --coassemble-output coassemble_dir --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --genomes genome_1.fna ...

# Example: update previous run to run specific coassemblies
ibis update --run-aviary --coassemblies coassembly_0 ... --coassemble-output coassemble_dir --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --genomes genome_1.fna ...