Phyluce Tutorials

• Tutorial I: UCE Phylogenomics
  • Download the data
  • Count the read data
  • Clean the read data
    • Quality control
  • Assemble the data
    • Assembly QC
  • Finding UCE loci
  • Extracting UCE loci
    • Exploding the monolithic FASTA file
  • Aligning UCE loci
    • Edge trimming
    • Internal trimming
  • Alignment cleaning
  • Final data matrices
  • Preparing data for downstream analysis
    • Downstream Analysis
  • Next Steps
• Tutorial II: Phasing UCE data
  • Exploding aligned and trimmed UCE sequences
  • Creating a re-alignment configuration file
    • [references]
    • [individuals]
    • [flowcell]
  • Mapping reads against contigs
  • Phasing mapped reads
• Tutorial III: Harvesting UCE Loci From Genomes
  • Starting directory structure
  • Download the data
    • chicken (galGal4)
    • alligator (allMis1)
  • Finding UCE loci
    • Get the UCE probes
    • Align the probes to the genomes
    • Extracting FASTA sequence matching UCE loci from genome sequences
    • Using the extracted sequences in downstream analyses
• Tutorial IV: Identifying UCE Loci and Designing Baits To Target Them
  • Starting directory structure
  • Data download and preparation
    • Download the genomes
    • Cleanup the genome sequences
    • Put genomes in their own directories
    • Convert genomes to 2bit format
    • Simulate reads from genomes
  • Read alignment to the base genome
    • Prepare the base genome
    • Align reads to the base genome
    • What it all means
  • Conserved locus identification
    • Convert BAMS to BEDS
    • Sort the converted BEDs
    • Merge overlapping or nearly-overlapping intervals
    • Remove repetitive intervals
    • Determining locus presence in multiple genomes
    • Determining shared, conserved, loci
  • Conserved locus validation
    • Extract FASTA sequence from base genome for temp bait design
    • Design a temporary bait set from the base taxon
    • Remove duplicates from our temporary bait set
    • Align baits against exemplar genomes
    • Extract sequence around conserved loci from exemplar genomes
    • Find which loci we detect consistently
  • Final bait set design
    • Design a bait set using all exemplar genomes (and the base)
    • Remove duplicates from our bait set
  • The master bait list
    • Subsetting the master probe list
  • In-silico test of the bait design
    • Align our bait set to the extant genome sequences
    • Match contigs to baits
    • Get match counts and extract FASTA information
    • Align the conserved locus data
    • Trim the conserved locus alignments
    • Remove the locus names from each alignment
    • Get stats across the aligned loci
    • Generate an incomplete matrix
    • Prep raxml files, run raxml ML searches, and reconcile best tree w/ bootreps