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BWA-FastAlign
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Add test datasets in README

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## 📖 Usage
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).
0. **Download Datasets.** We download E.coli reference genome and sequencing reads.
```bash
# This will generate the Hybrid Index files
# Download reference genome
wget http://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/005/845/GCA_000005845.2_ASM584v2/GCA_000005845.2_ASM584v2_genomic.fna.gz
gzip -d GCA_000005845.2_ASM584v2_genomic.fna.gz
mv GCA_000005845.2_ASM584v2_genomic.fna ref.fasta
# Download sequencing reads
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR258/003/SRR2584863/SRR2584863_1.fastq.gz -O reads_1.fq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR258/003/SRR2584863/SRR2584863_2.fastq.gz -O reads_2.fq.gz
```
1. **Index the Reference.** Before alignment, you must index your reference genome.
```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
./fastalign mem ref.fa reads.fq.gz > aln.sam
# Paired-end alignment
./fastalign mem ref.fa read1.fq read2.fq > aln.sam
./fastalign mem ref.fa read1.fq.gz read2.fq.gz > aln.sam
# Using multiple threads (Recommended: 32-128 threads for high throughput)
./fastalign mem -t 64 ref.fa read1.fq read2.fq > aln.sam
./fastalign mem -t 64 ref.fa read1.fq.gz read2.fq.gz > aln.sam
```
3. **Options.** BWA-FastAlign supports the standard BWA-MEM options. Run ./fastalign mem to see the full list.