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illumina

A reproducible Snakemake workflow for end-to-end de novo assembly and quality control of bacteriophage Illumina sequencing datasets. Starting from raw paired-end reads, the pipeline produces assembled genomes, virome classification scores, completeness estimates, terminal-repeat predictions, and a unified HTML + PDF report. A reproducible Snakemake workflow for end-to-end de novo assembly and quality control of bacteriophage Illumina sequencing datasets. Starting from raw paired-end reads, the pipeline produces assembled genomes, virome classification scores, completeness estimates, and a unified HTML + PDF report.

Illumina bacterial assembly snakemake is a snakemake pipeline to assemble lots of bacterial genomes from Illumina paired-end short-reads (typically 150bp); It also performs several QC steps on the reads and on the resulting assemblies. Everything needed can be found in this repository (except for the GTDB reference database for taxonomic assembly classification and the Kraken2 database for taxonomical read classification).