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1. bactopia/bactopia bactopia/bactopia Public

   A flexible pipeline for complete analysis of bacterial genomes

   Nextflow 418 72

2. camlhmp camlhmp Public

   🐪Classification through yAML Heuristic Mapping Protocol 🐪

   Python 8 2

3. dragonflye dragonflye Public

   🐉 🪰 Assemble bacterial isolate genomes from Nanopore reads

   Perl 117 10

4. fastq-dl fastq-dl Public

   Download FASTQ files from SRA or ENA repositories.

   Python 280 25

5. fastq-scan fastq-scan Public

   Output FASTQ summary statistics in JSON format

   C++ 29 1

6. sccmec sccmec Public

   A tool for typing SCCmec cassettes in assemblies

   Python 2