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hafeezakinniyi / bacterial-isolate-wgs-pipeline

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A modular, reproducible, and automated Bash pipeline for bacterial isolate whole-genome sequencing analysis from Illumina paired-end reads, including quality control, taxonomic classification, genome assembly, genome characterization, and coverage estimation.

linux bash bioinformatics genomics amr microbiology mlst wgs spades samtools whole-genome-sequencing bowtie2 antimicrobial-resistance quast kraken2 bracken abricate checkm bacterial-genomics amrfinderplus
  • Updated Aug 20, 2026
  • Shell

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