From 98f8a27a7ccd949886999c125b0e3e0028c63ede Mon Sep 17 00:00:00 2001 From: Yewen Li Date: Sun, 4 Jan 2026 00:09:48 +0800 Subject: [PATCH] Rename FastAlign to BWA-FastAlign in README --- README.md | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index e9bac15..69de9a3 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ -# FastAlign: Faster and Cheaper Sequence Alignment on Commercial CPUs +# BWA-FastAlign: Faster and Cheaper Sequence Alignment on Commercial CPUs -**FastAlign** is a high-performance, cost-efficient software package for mapping low-divergent sequences against a large reference genome, such as the human genome. +**BWA-FastAlign** is a high-performance, cost-efficient software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It is designed as a drop-in replacement for the de facto standard **BWA-MEM**, offering **2.27× ∼ 3.28× throughput speedup** and **2.54× ∼ 5.65× cost reductions** on standard CPU servers, while guaranteeing **100% identical output** (SAM/BAM) to BWA-MEM. @@ -14,7 +14,7 @@ It is designed as a drop-in replacement for the de facto standard **BWA-MEM**, o ## 🔧 Technical Innovations -FastAlign revitalizes the traditional alignment pipeline with two core algorithmic contributions: +BWA-FastAlign revitalizes the traditional alignment pipeline with two core algorithmic contributions: 1. **Multi-Stage Seeding (Hybrid Index)** * Combines **Kmer-Index**, **FMT-Index** (Enhanced FM-Index with prefetching), and **Direct-Index**. @@ -22,7 +22,7 @@ FastAlign revitalizes the traditional alignment pipeline with two core algorithm * Achieves an **18.92× improvement in memory efficiency** (bases processed per GB per second). 2. **Intra-Query Parallel Seed-Extension** - * Unlike BWA-MEM2 (which uses inter-query parallelism and suffers from load imbalance), FastAlign parallelizes the Smith-Waterman alignment *within* a single query. + * Unlike BWA-MEM2 (which uses inter-query parallelism and suffers from load imbalance), BWA-FastAlign parallelizes the Smith-Waterman alignment *within* a single query. * Includes **Dynamic Pruning** to skip zero-alignment scores. * Implements a **Sliding Window** mechanism to reduce costly memory gather operations. * Achieves **3.45× higher SIMD utilization**, performing consistently well on both WGS (Whole Genome Sequencing) and WES (Whole Exome Sequencing) data. @@ -37,13 +37,13 @@ FastAlign revitalizes the traditional alignment pipeline with two core algorithm ### Compilation ```bash -git clone https://github.com/your-username/FastAlign.git -cd FastAlign +git clone https://github.com/your-username/BWA-FastAlign.git +cd BWA-FastAlign make ``` ## 📖 Usage -FastAlign follows the same command-line interface as BWA-MEM. +BWA-FastAlign follows the same command-line interface as BWA-MEM. 1. **Index the Reference.** Before alignment, you must index your reference genome (e.g., human_g1k_v37.fasta). ```bash @@ -63,10 +63,10 @@ FastAlign follows the same command-line interface as BWA-MEM. ./fastalign mem -t 64 ref.fa read1.fq read2.fq > aln.sam ``` -3. **Options.** FastAlign supports the standard BWA-MEM options. Run ./fastalign mem to see the full list. +3. **Options.** BWA-FastAlign supports the standard BWA-MEM options. Run ./fastalign mem to see the full list. ## 📜 Citation -If you find FastAlign is useful in your research, please cite our paper: +If you find BWA-FastAlign is useful in your research, please cite our paper: ```bibtex @inproceedings{fastalign2026, title={Faster and Cheaper: Pushing the Sequence Alignment Throughput with Commercial CPUs},