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sanger-pathogens / snp-sites

Finds SNP sites from a multi-FASTA alignment file
http://sanger-pathogens.github.io/snp-sites/
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Recommended workflow? #71

Open stevendavis opened 6 years ago

stevendavis commented 6 years ago

What is the recommended workflow to produce a VCF file when starting with two unaligned bacterial whole-genome fasta files, each approximately 3 million nucleotides? Any particular aligner and file format conversion utilities you can recommend?