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1. nextera_cleaner nextera_cleaner Public

   Script to clean Illumina pair-end sequences produced with the Nextera kit. Bases below Q30, Ns, and Nextera adapters are removed. Bases can also be removed at the beginning and end of each sequence…

   Shell 2

2. pair-end_cleaner pair-end_cleaner Public

   Script to unzip, clean, assemble, and convert illumina pair-end fastq files in all subdirectories for 16S amplicon data (V3, V4 and V3-V4 regions).

   2

3. metagenomic_pipeline metagenomic_pipeline Public

   Description of the metagenomic pipeline we have for analysis of 16S and 18S amplicon NGS

   2

4. VF_classifier VF_classifier Public

   A comprehensive tool for identifying and classifying virulence factors in bacterial genomes using BLAST against the VFDB Virulence Factor Database, with automated visualization and interactive repo…

   Python