I am a beginner. I want to learn BWA and MAQ. My question is that where I can download the ref.fasta and read.fastq file, which should be a small genome because the small memory in my computer.
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Look for reference genomes in NCBI. MAQ is nice because it does a lot of things for you, but it's been superseded by other software suites. bwa for alignment and either SAMTools or GATK would be more useful in the long run. MAQ's algorithm is also much slower than bwa, but it won't matter much for something small, like a bacterium. -
swbarnes2,
Thanks a lot.Comment
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