Home

HashBrown assembles bacterial genomes from Nanopore long reads, Illumina (or Ion Torrent) short reads, or both, and ends every run with QC and a per-sample HTML/PDF report: stage-by-stage read and assembly funnels, coverage, consensus QV, species confirmation, completeness, typing, AMR genes, annotation and contamination screens (Methods has the full list; the deeper modules are optional and auto-detected). Like its namesake — shredded potatoes pressed into one piece — it presses reads into one assembly. It merges and supersedes BGA and BGA_short.

The three ways to run it

hashbrown -l nanopore_fastq/ -o results/                      # long reads only
hashbrown -l nanopore_fastq/ -s illumina_fastq/ -o results/   # hybrid (short reads polish)
hashbrown -s illumina_fastq/ -o results/                      # short reads only

Pages

• Installation — conda, pip, troubleshooting
• Usage — inputs, options, resuming, performance
• Methods — what each step runs and why, with references
• Outputs — folders and files
• Validation — benchmarking the polisher combinations against a gold standard
• FAQ — troubleshooting
• Development — tests, CI, releases