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docs/workflow/consensus_qc.md

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@@ -10,7 +10,7 @@ Within the MultiQC report, Viralgenie provides a number of custom tables based o
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- [QUAST](#quast): QUAST is a quality assessment tool for genome assemblies. It calculates various metrics such as N50, L50, number of contigs, and total length.
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- [CheckV](#checkv): CheckV is a tool for assessing the quality of metagenome-assembled viral genomes. It calculates various metrics such as completeness, contamination, and strain heterogeneity.
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- [Prokka](#prokka): Prokka is a whole genome annotation pipeline for identifying features of interest in a set of genomic DNA sequences, and labelling them with useful information.
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- [blastn](#blastn): BLAST is a tool for comparing primary biological sequence information. It calculates the similarity between the consensus genome and the reference genome.
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- [blastn](#blast): BLAST is a tool for comparing primary biological sequence information. It calculates the similarity between the consensus genome and the reference genome.
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- [mmseqs-search](#mmseqs-search) - included as 'annotation': MMseqs is an ultra-fast and sensitive search tool for protein and nucleotide databases. Viralgenie uses MMseqs to annotate the consensus genomes and assign them a species name, segment name, expected host, etc.
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- [mafft](#mafft): MAFFT is a multiple sequence alignment program.
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