SweepGA

Fast genome alignment with plane sweep filtering. Wraps FastGA aligner and applies plane sweep filtering to keep the best non-overlapping alignments.

What it does

SweepGA can either:

1. Align FASTA files directly using integrated FastGA (supports .fa.gz)
2. Filter existing PAF alignments from any aligner (wfmash, minimap2, etc.)

By default, it applies 1:1 plane sweep filtering to keep the single best mapping per query-target chromosome pair.

Tools Included

This package includes two binaries:

• sweepga - Genome alignment and filtering tool
• alnstats - Alignment statistics and validation tool

Use alnstats to verify filtering results:

# Show statistics for a PAF file
alnstats alignments.paf

# Compare before/after filtering
alnstats raw.paf filtered.paf

# Detailed per-genome-pair breakdown
alnstats alignments.paf -d

Installation

Requires Rust 1.70+. Clone and install:

git clone https://github.com/pangenome/sweepga.git
cd sweepga
cargo install --force --path .

Build Issues on Mixed glibc Systems

Symptoms: Build fails with linker errors like:

ld: /usr/lib/x86_64-linux-gnu/librt.so: undefined reference to '__pthread_barrier_wait@GLIBC_PRIVATE'

This occurs on systems with multiple package managers (e.g., Debian + Guix) providing different glibc versions.

Fix: Use the clean build script to isolate from environment conflicts:

./scripts/build-clean.sh --install

See docs/BUILD-NOTES.md for details.

With Guix

Adapted from https://issues.genenetwork.org/topics/rust/guix-rust-bootstrap:

# Update Guix
mkdir -p $HOME/opt
guix pull -p $HOME/opt/guix-pull-20251012 --url=https://codeberg.org/guix/guix

# Be sure to use the updated Guix
alias guix=$HOME/opt/guix-pull-20251012/bin/guix

# Update Rust and Cargo
mkdir -p ~/.cargo ~/.rustup # to prevent rebuilds
guix shell --share=$HOME/.cargo  --share=$HOME/.rustup -C -N -D -F -v 3 guix gcc-toolchain make libdeflate pkg-config xz coreutils sed zstd zlib nss-certs openssl curl
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
. ~/.cargo/env
rustup default stable
exit

# Clone the repository
git clone https://github.com/pangenome/sweepga.git
cd sweepga

guix shell --share=$HOME/.cargo  --share=$HOME/.rustup -C -N -D -F -v 3 guix gcc-toolchain make libdeflate pkg-config xz coreutils sed zstd zlib nss-certs openssl curl cmake clang # we need cmake and clang too for building
. ~/.cargo/env
export LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib
cargo build --release

# Check the lib path and put it into your ~/.bashrc or ~/.zshrc
echo $GUIX_ENVIRONMENT/
   #/gnu/store/whgjblccmr4kdmsi4vg8h0p53m5f7sch-profile/
exit
echo "export GUIX_ENVIRONMENT=/gnu/store/whgjblccmr4kdmsi4vg8h0p53m5f7sch-profile/" >> ~/.bashrc # or ~/.zshrc
source ~/.bashrc # or ~/.zshrc

# Use the executable in sweepga/target/release
env LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib ./target/release/sweepga --help

Basic Usage

Direct alignment (FASTA input)

# Self-alignment with 1:1 filtering
sweepga genome.fa.gz > output.paf

# Pairwise alignment (target, query order)
sweepga target.fa query.fa > output.paf

# With 2 threads
sweepga genome.fa.gz -t 2 > output.paf

PAF filtering (pipe from stdin)

# Default: 1:1 plane sweep filtering
cat alignments.paf | sweepga > filtered.paf

# Keep best mapping per query only (1:∞)
cat alignments.paf | sweepga -n 1 > filtered.paf

# No filtering, just pass through
cat alignments.paf | sweepga -n many > output.paf

Reading PAF files directly

# Read from file instead of stdin
sweepga alignments.paf > filtered.paf

Example: 8 yeast genomes

# Direct alignment and filtering in one step
sweepga data/scerevisiae8.fa.gz > scerevisiae8.paf

# Result: ~26K mappings (1:1 filtered)
# - Each genome pair gets best alignment per chromosome pair
# - Self-mappings excluded by default (use --self to include)

Parameters

-n/--num-mappings - n:m-best mappings in query:target dimensions (default: 1:1)

• "1:1" - Orthogonal: keep best mapping on both query and target axes
• "1" - Keep best mapping per query position only
• "many" - No filtering, keep all mappings
• "n:m" - Keep top n per query, top m per target (use ∞/many for unbounded)

-o/--overlap - Maximum overlap ratio (default: 0.95)

• Mappings with >95% overlap with a better-scoring mapping are removed

-l/--min-block-length - Minimum alignment block length (default: 0)

-i/--min-identity - Minimum identity threshold (0-1 fraction, 1-100%, or "aniN")

-t/--threads - Number of threads (default: 8)

--self - Include self-mappings (excluded by default)

-f/--no-filter - Disable all filtering

How It Works

The plane sweep algorithm operates per query-target chromosome pair:

1. Sort mappings by query position
2. Score each mapping: identity × log(block_length) (matches wfmash)
3. Sweep left-to-right, keeping best mappings based on -n setting:
   • 1:1: Keep single best mapping per position on both query and target
   • 1: Keep best mapping per query position (multiple targets allowed)
   • many: Keep all non-overlapping mappings
4. Filter mappings with >95% overlap (configurable with -o)

Citation

SweepGA: Fast plane sweep filtering for genome alignments https://github.com/pangenome/sweepga