Documentation ¶
Overview ¶
Implementation (work in progress) of the resequencing analysis pipeline used to teach the introductory NGS bioinformatics analysis course at SciLifeLab as described on this page: http://uppnex.se/twiki/do/view/Courses/NgsIntro1502/ResequencingAnalysis.html
Prerequisites: Samtools, BWA, Picard, GATK. You can install all tools except GATK on X/L/K/Ubuntu, with this command:
sudo apt-get install samtools bwa picard-tools
GATK needs to be downloaded and installed manually from: http://www.broadinstitute.org/gatk
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