Introduction

High-Performance Bioinformatics I/O for Mojo

GitHub · API Reference · PyPI

BlazeSeq is a cohesive parsing stack for genomics formats in Mojo. It is designed for the full path from local files to accelerated compute with high throughput, explicit data ownership, and GPU-ready batch layouts.

Why BlazeSeq

• One stack, multiple formats: FASTQ, FASTA, FAI, and BED in one library.
• Performance by default: SIMD-oriented parsing and low-allocation APIs.
• CPU to GPU bridge: Batch APIs and upload utilities for accelerator workflows.
• Ergonomic interfaces: Stream views, owned records, or batch iteration from the same parser.

Supported Formats

Format	Parser	Typical use
FASTQ	FastqParser	Read sequencing reads with quality scores
FASTA	FastaParser	Reference and assembly sequence parsing
FAI	FaiParser	FASTA/FASTQ index metadata access
BED	BedParser	Genomic interval and region processing

Quick Start

Install via pixi by adding BlazeSeq to your pixi.toml:

[dependencies]
blazeseq = { git = "https://github.com/MoSafi2/BlazeSeq", branch = "main" }

Then run pixi install and parse FASTQ data:

from blazeseq import FastqParser, FileReader
from std.pathlib import Path

def main() raises:
    var parser = FastqParser[FileReader](FileReader(Path("reads.fastq")), "sanger")
    for view in parser.views():
        _ = view.id()
        _ = len(view)

Parser Workflows

FASTA

from blazeseq import FastaParser, FileReader
from std.pathlib import Path

def main() raises:
    var parser = FastaParser[FileReader](FileReader(Path("ref.fa")))
    for record in parser:
        print(record.id(), len(record))

FAI

from blazeseq import FaiParser, FileReader
from std.pathlib import Path

def main() raises:
    var parser = FaiParser[FileReader](FileReader(Path("ref.fa.fai")))
    for rec in parser:
        print(rec.name(), rec.length(), rec.offset())

BED

from blazeseq import BedParser, FileReader
from std.pathlib import Path

def main() raises:
    var parser = BedParser[FileReader](FileReader(Path("regions.bed")))
    for interval in parser.views():
        print(interval.chrom(), interval.chrom_start, interval.chrom_end)

GPU Pipeline Example

RapidgzipReader currently preserves the older API but falls back to GZFile internally while the external rapidgzip dependency is disabled.

from blazeseq import FastqParser, RapidgzipReader
from std.pathlib import Path

def main() raises:
    var reader = RapidgzipReader(Path("reads.fastq.gz"), parallelism=4)
    var parser = FastqParser[RapidgzipReader](reader^, "illumina_1.8")
    for batch in parser.batches(1024):
        var device_batch = batch.to_device()
        _ = device_batch

Next Steps

• Explore the complete API Reference.
• Run end-to-end examples in examples/.
• Review benchmark tooling in benchmark/.