SegPE

A simple program for classifing and separating paired-ends (PE) FASTQ after removing adapters via adapter-index seq

Major algorithms:

• Exact match search: This is a more direct method for finding exact matches of artificial sequences. Regular expression matching and Hamming distance: This is suitable for detecting and locating index sequences, especially when mismatches of a certain length are taken into account.
• Process and classify PE sequences: After removing the adapter and index sequences, classify the PE sequences and create new PE FASTQ files.
• Use Multi-threads, SIMD and AsyncIO to handle large amounts of data.

Setup

# Install rust
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
# or update
rustup update

cd SegPE
cargo build --release

## SIMD  edit Cargo.toml first
# Intel x86
cargo build --features simd_avx2 --release
# Arm 
cargo build --features simd_neon --release

Example:

time RUST_LOG=INFO ./target/release/segpe --five-art-fa data/5_art.fa --three-art-fa data/3_art.fa --five-idx-fa data/idx.fa --pe1-fastq data/PE1.fastq.gz --pe2-fastq data/PE2.fastq.gz -n 1000 -b 100 -o data/output

Version

0.1.14, build-240429

Usage

飞书文档

Notion中文文档

Notion Usage

License

^Licensed under either of Apache License, Version 2.0 or MIT license at your option.^ Unless you explicitly state otherwise, any contribution intentionally submitted for inclusion in this crate by you, as defined in the Apache-2.0 license, shall be dual licensed as above, without any additional terms or conditions.