MemPanG23

MemPanG23 Assembly & Evaluation

• Part 1 Assembly
• Part 2 Evaluation

Tools we will use for this course

1. Understand my genome - Meryl v1.4 (recommend to install with gcc 10+)
2. Create an assembly - Verkko v1.3.1 (recommend to install through conda)
3. Check the assembly graph on BandageNG (local)
4. Label chromosomes, find telomeres - MashMap v2.0, seqtk v1.4
5. Align long-reads back to the assembly - Winnowmap2 v2.03, Samtools v1.17
6. Collect anomalies Merqury (clone latest from github; has dependencies on R v4.3.0 (argparse, ggplot2, and scales), Bedtools v2.30.0, Java Runtime Environment) T2T-Polish (clone latest from github; no additional installation required for this course) seqrequester (clone latest on github and install with gcc 10+)
7. Browse through the data with IGV v2.16.1 (local). I prefer the IGV and IGV Command Line Version to easily manipulate memory limit.
8. Browse through some real issues on HG002 diploid assembly with IGV (local, if time permits)

Where is the data?

All the input and results are available under a_thal.
Feel free to check the results here and compare to yours.

Note: Raw input sequence data (*.fq.gz files) is available under /opt/assembly_data/

Some environment variables to set up for convenience

export MERQURY=/opt/merqury
export T2T_Polish=/opt/T2T-Polish
export tools=/opt

We will work in day3_assembly_evaluation.

mkdir -p ~/day3_assembly_evaluation
cd day3_assembly_evaluation