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- Using the Integrative Genomics Viewer (IGV)
- Shell Scripting
- Mapped read data evaluation (SAMtools)
- Installing Linux tools
- Identifying mutations in microbial genomes (breseq)
- Calling variants in diploid genomes
- Annotating variants
— - Structural variation
- Genome variation in mixed samples (FreeBayes, deepSNV)
- SRA toolkit, UCSC Genome Browser
- Practical advice - short read re-sequencing data
- Variant calling with GATK
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