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bio-metagenomics-kraken

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Taxonomic classification of metagenomic reads using Kraken2. Fast k-mer based classification against RefSeq database. Use when performing initial taxonomic classification of shotgun metagenomic reads before abundance estimation with Bracken.

When to use

• initial taxonomic classification of shotgun metagenomic reads
• assign taxonomic labels to sequencing reads
• build custom Kraken2 database
• add custom sequences to library
• inspect database contents
• parse Kraken output in Python
• filter report by rank

When not to use

• abundance estimation with Bracken
• marker-based profiling
• metagenome visualization

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