From 643832af098fbf8e4466dc034f34a0cb16e18465 Mon Sep 17 00:00:00 2001
From: Yewen Li <liyewen521@gmail.com>
Date: Thu, 11 Dec 2025 18:41:20 +0800
Subject: [PATCH] Revise README to enhance documentation and clarity

Expanded README with detailed features, installation instructions, and usage examples for FastAlign.
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 README.md | 82 +++++++++++++++++++++++++++++++++++++++++++++++++------
 1 file changed, 74 insertions(+), 8 deletions(-)

diff --git a/README.md b/README.md
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-# FastAlign
-Fast alignment tool based on bwa-mem
+# FastAlign: Faster and Cheaper Sequence Alignment on Commercial CPUs
 
-# 1. Compile the source code
-make -j 8
+**FastAlign** is a high-performance, cost-efficient software package for mapping low-divergent sequences against a large reference genome, such as the human genome.
 
-# 2. Build the FMT-Index
-./fastalign index reference.fasta
+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.
 
-# 3. Run sequence alignment with FastAlign
-./fastalign mem -t 64 -2 -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:fastbwa reference.fasta r1.fq.gz r2.fq.gz
+## 🚀 Key Features
+
+*   **High Throughput:** Achieves ~2.85× average speedup over BWA-MEM by optimizing both the seeding and extension phases.
+*   **Cost Efficient:** Delivers 2.54× ∼ 5.65× cost reduction compared to state-of-the-art CPU and GPU baselines (including BWA-MEM2 and BWA-GPU).
+*   **Identical Output:** Guarantees 100% output compatibility with BWA-MEM. You can swap it into your existing pipelines without changing downstream analysis results.
+*   **Low Memory Footprint:** Uses a novel Multi-stage Seeding strategy (Hybrid Index) that improves search performance without the massive memory overhead seen in hash-based or learned-index aligners (e.g., ERT-BWA-MEM2).
+*   **Optimized for Modern CPUs:** Features an Intra-query Parallel algorithm for the seed-extension phase, utilizing AVX2 instructions to eliminate computation bubbles caused by varying read lengths.
+
+## 🔧 Technical Innovations
+
+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**.
+    *   Dynamically switches strategies based on seed length and match density.
+    *   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.
+    *   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.
+
+## 📥 Installation
+
+### Prerequisites
+*   Linux operating system (tested on Ubuntu 22.04).
+*   GCC compiler (version 11.4 or higher recommended).
+*   CPU supporting **AVX2** instructions (most modern Intel/AMD CPUs).
+*   zlib development files.
+
+### Compilation
+```bash
+git clone https://github.com/your-username/FastAlign.git
+cd FastAlign
+make
+```
+
+## 📖 Usage
+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
+# This will generate the Hybrid Index files
+./fastalign index ref.fa
+```
+
+2.  **Align Reads (Mem).** Map single-end or paired-end reads to the reference.
+```bash
+# Single-end alignment
+./fastalign mem ref.fa reads.fq > aln.sam
+
+# Paired-end alignment
+./fastalign mem ref.fa read1.fq read2.fq > aln.sam
+
+# Using multiple threads (Recommended: 32-128 threads for high throughput)
+./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.
+
+## 📜 Citation
+If you find 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},
+  author={Zhonghai Zhang, Yewen Li, Ke Meng, Chunming Zhang, Guangming Tan},
+  booktitle={Proceedings of the 31st ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP '26)},
+  year={2026}
+}
+```