A bash script and eLabNotes for the BWA-MEM + GATK pipeline I'm assembling for Eukaryotic haploid genome WGS analysis. I'll be keeping detailed notes here on what our rationale is for the analyses we do, and I'll be keeping relevant code snippets as well as the evolving bash pipeline for assembling the reads, cleaning the assembly, SNP-calling, and SNP-filtering.
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A bash script for the GATK pipeline I'm developing for Plasmodium WGS analysis.
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