An easy to use for wrapper for a robust snakemake pipeline for metagenomic hybrid assembly, binning, and annotation. The pipeline currently includes a step-down iterative hybrid assembler, an isolate hybrid assembler, a quality control module and a comprehensive binning pipeline. Each module can be run independently or as a single pipeline depending on provided input.

Module details

batchPerforms all steps in the Aviary pipeline on a batch file. Clusters the final output.
clusterDereplicate/choose representative genomes from multiple aviary runs
assemblePerform quality control and assembly of provided reads. Will provide hybrid assembly if given long and short reads
recoverRecover MAGs from provided assembly using a variety of binning algorithms. Also perform quality checks on recovered MAGs and taxonomic classification.
annotateProvide taxonomic and functional annotations for a given set of MAGs
diversityUse lorikeet to calculate strain diversity statistics on a set of MAGs and reads
completePerforms the complete workflow up to last possible rule given the provided inputs
isolatePerforms hybrid isolate assembly. For use with isolated pure sequencing results.
configureSet or reset environment variables used by aviary



On its way :P


Code is GPL-3.0



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