Need a software advice and a sample/example in Python or Ruby script which runs BBMap then SAM tools and generates mutation report
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6.8 years ago
vassialk ▴ 200

Need a sample/example in Python or Ruby/Java or C# script which runs BBMap or BWA/Bowtie then SAM or GATK tools and generates mutation report. Want to find mutations from tuberculosis contigs against a whole genome reference, have used NextGene, now looking for command line tools, please advise what software to choose for a pipeline. Thx.

softwa wgs sequencing • 1.4k views
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