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@apeltzer apeltzer released this May 6, 2019

Initial release of nf-core/bacass, created with the nf-core template.

This pipeline is for bacterial assembly of next-generation sequencing reads. It can be used to quality trim your reads using Skewer and performs basic QC using FastQC. Afterwards, the pipeline performs read assembly using Unicycler and assesses assembly quality using QUAST. Contamination of the assembly is checked using Kraken2 to verify sample purity. The resulting bacterial assembly is annotated using Prokka.

Furthermore, the pipeline creates various reports in the results directory specified, including a MultiQC report summarizing some of the findings and software versions.

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