Quick Start

Strain-level metagenomics in three commands. ZipStrain maps reads, profiles them at single-nucleotide resolution, and compares samples by ANI to tell whether they share a strain.

Install

# Conda (recommended — bundles samtools and the map aligners)
conda create -n zipstrain -c conda-forge -c bioconda python=3.12 zipstrain bowtie2 samtools sylph
conda activate zipstrain
zipstrain test

Prefer pip? pip install zipstrain (then install samtools separately). Full options: Installation.

The three commands

1. map — reads → BAMs

Aligns reads to a reference and writes sorted BAMs plus a samples.txt ready for profiling. Omit --reference-fasta to let Sylph pick and build a reference automatically. Resumable if interrupted.

zipstrain map -i reads.csv -o mapped \
  --reference-fasta ref.fna --stb-file ref.stb

2. profile — BAMs → nucleotide profiles

Counts A/C/G/T at every reference position and writes per-genome stats (coverage, breadth, a present/absent call) and SNVs. Missing assets are auto-generated and cached.

zipstrain profile -i mapped/samples.txt -f ref.fna -s ref.stb -r profiled

3. compare — profiles → ANI

Compares every pair of samples by popANI (near 100% ⇒ same strain). Point --profile-db at a CSV of profile_name,profile_location.

zipstrain compare --profile-db profiles.csv -r compared

Every run writes a zipstrain_run.log so you can tell if it is running, finished, or crashed.

Next steps

• Tutorial — worked end-to-end examples (CLI and Nextflow)
• Expected output — every output file and column explained
• User Manual — full command reference and the Nextflow pipeline