☰ Menu

      Genome Assembly Workshop 2020

Home
Introduction and Lectures
Intro to the Workshop and Core
Schedule
Genome Assembly
Introduction to the DNA Tech Core
A Brief Overview of Genome Annotation, with a Focus on the Use of Isoseq
Support
Cheat Sheets
Software and Links
Scripts
Prerequisites
CLI - Logging in and Transferring Files
CLI - Intro to Command-Line
CLI - Advanced Command-Line (extra)
CLI - Running jobs on the Cluster and using modules
Conda
R - Getting Started
R - Intro to R
R - Prepare Data in R (extra)
R - Data in R (extra)
More Materials (extra)
Snakemake
Introduction
Challenge Answers
K-mers
K-mers tutorial
PacBio
Introduction to PacBio HiFi Data and Applications
Genome Assembly with PacBio HiFi Data
Improved Phased Assembly (IPA) Using HiFi Data
Assembling the drosophila genome with IPA and HiFi data
ONT Assembly
Introduction to ONT
Assembly using ONT - Hands-on
Bionano
Optical mapping for accurate genome assembly, comparative genomics, and haplotype segregation
Phase Genomics
Using Proximity to Fix Assembly
Genome Assessment
BUSCO
Additional QA/QC and metrics
ETC
Closing thoughts
Workshop Photos
Github page
Report Errors
Biocore website

Answers to challenge activities and CLI/cluster warmup

  1. Win scp, filezilla or secure copy (scp)
  2. samples = ["A", "B", "C"] https://snakemake.readthedocs.io/en/stable/project_info/faq.html#how-do-i-remove-all-files-created-by-snakemake-i-e-like-make-clean OR rm -rf calls/ mapped/ plots/
  3. shell:
        "module load samtools; "
        "module load bcftools; "
    
  4. rule vcf_tsv:
    input:
        "calls/all.vcf"
    output:
        "calls/vcf.tsv"
    shell:
        "sed '/##/d' {input} > {output}" 
    
rule all:
    input:
        "calls/all.vcf",
        "plots/quals.svg",
        "calls/vcf.tsv"

OR

   "sed '1,28d' {input} > {output}"
  1. temp() on the sort rule output like bwa rule.