hackmd-github-sync-badge This pipeline was developed for mammal genomes and includes some steps that are necessary for assembling these larger (~3Gb) genomes but that may not be needed for smaller genomes. Table of Contents Step 1: Run Hifiasm The first step is to use the HiFiasm software to assemble a genome from the raw PacBio reads. (You'll start with the slurm part at the top, as always). Then, the general structure for assembly of heterozygous genomes is: hifiasm -o prefix -t numberThreads input.fasta.gz --write-paf --write-ec /dev/null

This pipeline is designed for modern DNA of non-model organisms but does use a reference genome for alignment. :bird: Table of Contents Part I: Read filtering, assembly, quality control Step 1: Check the quality of samples and trim/filter accordingly 1a. Check the md5 for each file to make sure it downloaded/uploaded correctly. md5sum sample1_R1.fastq.gz or, to run in a loop (best done within a batch script for multiple large files; see step 1b for detailed structure of a batch script):

Intro to bash computing hackmd-github-sync-badge This tutorial will get us started with basic bash tools that will help us process and analyze genomic data. Auto-generated Table of Contents A Note on Computing Increasingly, biological research requires competent computing skills including the ability to install and use command-line programs. The only way to learn computing skills is to practice them! However, you don't need to practice by yourself, especially as you are getting started. Computing is collaborative: When you run into a problem, talk about your code with your classmates, read about similar problems on StackOverflow, and spend time on Google learning about how other people have solved the problems. Consider these challenges to be learning opportunities. :female-student: :memo:

hackmd-github-sync-badge :ear_of_rice: :dog2: The goal of this pipeline is to detect evolutionary signatures of selection that will enable the determination of the genetic basis of a phenotype (e.g., plague resistance in prairie dogs). The pipeline starts with a filtered vcf file, which we generated previously, and conducts tests for selection within genomes in a small sample. Table of Contents I. GWAS in plink :::warning

Note: This material is generated from the publicly available resources from the Woods Hole Molecular Evolution course. Credit goes to the instructors of that course. Table of Contents Note: IQ-Tree is installed as a conda environment in our /project/ directory. I named the environment 'IQt_env'.:female-teacher: We will use a subset of data presented in Chiari et al. 2012. Those data are in our /project/ directory, but you also will want to download the fasta file to take a look at the aligned sequences on your own computer. :turtle: Let's get started! :turtle: Step 1: View the alignment on your computer Open the alignment (fasta) file in MEGA and the partition (nexus) file in BBEdit/Notepad.