A simple bacterial assembly and annotation pipeline
Short Read Assembly
This pipeline is primarily for bacterial assembly of next-generation sequencing reads. It can be used to quality trim your reads using Skewer and performs basic sequencing QC using FastQC. Afterwards, the pipeline performs read assembly using Unicycler. Contamination of the assembly is checked using Kraken2 to verify sample purity.
Long Read Assembly
For users that only have Nanopore data, the pipeline quality
Creator: Andreas Wilm, Alexander Peltzer
Submitter: Finn Bacall