Page Index - barrettlab/2021-Genomics-bootcamp GitHub Wiki

43 page(s) in this GitHub Wiki:

• Home
• "Species tree" estimation
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• 2022 Biol 320 Lonicera japonica invasion history animation
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• 2022 Biol 320 Migseq data processing commands on myco server
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• 2022 Biol 320 Population genomic analyses with R
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• 2025 Biol 320 metagenomic analyses
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• Analysis of contemporary and historical population stucture and admixture with 'dystruct'
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• Home and schedule
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• I. Getting Started with UNIX
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• II. Illumina data quality
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• III. Assembling plastid genomes
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• iPyRAD introductory tutorial with simulated data with Maribeth Latvis
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• ISSRseq and downstream commands for River on myco server
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• IV. Lab Protocol for ISSR seq
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• Low coverage phenotype association with angsd
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• Plastid Genome Annotation with GeSeq
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• Population genomic analyses with sambaR
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• Preliminaries: Using the commandline, signing into a server, and submitting jobs to a HPC
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• Processing of whole plastid genomes, alignment, and partitioning for phylogenomic analysis
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• Running the ISSRseq pipeline for ISSR data or plastomes
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• Sequence capture data processing assembly with secapr
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• V. Running the ISSR seq data processing pipeline
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