pgr - Practical Genome Refiner

pgr is a command-line toolkit for working with genomes and genome-derived data: sequences, alignments, variation, and related formats.

It is designed as a practical “Swiss Army knife” for day-to-day bioinformatics workflows, with a focus on:

• Format-aware utilities for common genomics file types (FASTA/FASTQ/2bit, AXT/PSL/Chain/Net/MAF, GFF)
• Interoperable outputs (tabular conventions, FASTA/MAF for alignments)
• Pipeline-friendly behavior (stdin/stdout where possible, predictable output, composable subcommands)
• Performance and robustness (Rust implementation, zero-panic policy for malformed inputs)

High-level capabilities include:

• Sequences: FASTA/FASTQ inspection, filtering, slicing, conversion, 2bit querying, and pbit population archive compression
• Alignments: sorting, filtering, conversion, and coordinate/range utilities across UCSC formats
• Pangenome: PAF implicit graph indexing, querying, and conversion (BED/MAF/GFA/VCF)
• Pipelines & plots: integrated workflows (optionally using external tools) and LaTeX/TikZ figure generation

Install

Current release: 0.3.0

cargo install --path . --force #--offline

# test
cargo test -- --test-threads=1

Usage

After installation, the pgr binary should be available in your PATH:

pgr help
pgr fa --help
pgr fas --help

Examples

This repository contains many subcommands and end-to-end workflows. Extended and curated examples are collected in:

• docs/usage_examples.md

Below are a few quick examples to get started:

# Basic FASTA statistics
pgr fa size tests/fasta/ufasta.fa

# Block FA summary
pgr fas stat tests/fas/example.fas --outgroup

# 2bit range extraction
pgr 2bit range tests/genome/mg1655.2bit NC_000913:1-100

# Create a pbit population archive from a reference and sample assemblies
pgr pbit create -r tests/pgr/pseudocat.fa -i tests/pgr/pseudopig.fa -o tmp.pbit

# Extract a region from all samples in the archive
pgr pbit range tmp.pbit scaffold_1:1-1000 -o tmp.fa

External dependencies

Some subcommands depend on external executables:

• pgr pl ucsc requires the UCSC kent-tools suite, including programs such as faToTwoBit, axtChain, chainAntiRepeat, chainMergeSort, chainPreNet, chainNet, netSyntenic, netChainSubset, chainStitchId, netSplit, netToAxt, axtSort, axtToMaf, netFilter, netClass, and chainSplit.
• pgr pl trf depends on trf and spanr.
• pgr pl rept and pgr pl ir depend on FastK, Profex, and spanr.
• pgr pl p2m depends on spanr.
• pgr fas refine depends on an external multiple sequence alignment tool such as clustalw (default), muscle, or mafft.

Author

Qiang Wang wang-q@outlook.com

License

MIT.

Copyright by Qiang Wang.

Written by Qiang Wang wang-q@outlook.com, 2024-