Scalable telomere-to-telomere assembly with hifiasm

This session is part of Biodiversity Genomics Academy 2023

Session Leader(s)

Haoyu Cheng
Research Fellow in Biomedical Informatics, Harvard Medical School

Description

By the end of this session you will be able to:

1. Run hifiasm by yourself
2. Understand different types of assemblies
3. Understand how to improve the assembly quality when the results are not ideal

Prerequisites

1. Understanding the terms genome assembly, reads, contigs, genome graph
2. Understanding of linux command line basics

!!! warning "Please make sure you MEET THE PREREQUISITES and READ THE DESCRIPTION above"

You will get the most out of this session if you meet the prerequisites above.

Please also read the description carefully to see if this session is relevant to you.

If you don't meet the prerequisites or change your mind based on the description or are no longer available at the session time, please email tol-training at sanger.ac.uk to cancel your slot so that someone else on the waitlist might attend.

Connecting to gitpod for the session

Click here to launch a Gitpod workspace with hifiasm

Commands for the session

1. Let's assemble only with HiFi reads

cd /workspace/bin/HiFi

/usr/bin/time -v ../hifiasm -o HG002.chr11.10M -t4 ../HG002.HiFi.chr11.10M.fastq.gz &>>bp.asm.log

awk '/^S/{print ">"$2;print $3}' HG002.chr11.10M.bp.hap1.p_ctg.gfa > HG002.chr11.10M.bp.hap1.fa
awk '/^S/{print ">"$2;print $3}' HG002.chr11.10M.bp.hap2.p_ctg.gfa > HG002.chr11.10M.bp.hap2.fa

2. Let's assemble with HiFi reads and trio-binning

cd /workspace/bin/HiFi

/usr/bin/time -v ../hifiasm -o HG002.chr11.10M -t4 -1 HG002.pat.chr11.10M.yak -2 HG002.mat.chr11.10M.yak ../HG002.HiFi.chr11.10M.fastq.gz &>>trio.asm.log

awk '/^S/{print ">"$2;print $3}' HG002.chr11.10M.dip.hap1.p_ctg.gfa > HG002.chr11.10M.trio.hap1.fa
awk '/^S/{print ">"$2;print $3}' HG002.chr11.10M.dip.hap2.p_ctg.gfa > HG002.chr11.10M.trio.hap2.fa

3. Let's assemble with HiFi and Hi-C reads

cd /workspace/bin/HiFi

/usr/bin/time -v ../hifiasm -o HG002.chr11.10M -t4 --h1 ../HG002.HiC.chr11.10M.R1.fastq.gz --h2 ../HG002.HiC.chr11.10M.R2.fastq.gz ../HG002.HiFi.chr11.10M.fastq.gz &>hic.asm.log

awk '/^S/{print ">"$2;print $3}' HG002.chr11.10M.hic.hap1.p_ctg.gfa > HG002.chr11.10M.hic.hap1.fa
awk '/^S/{print ">"$2;print $3}' HG002.chr11.10M.hic.hap2.p_ctg.gfa > HG002.chr11.10M.hic.hap2.fa

4. Evaluate phasing errors:

cd /workspace/bin/HiFi

../yak trioeval -t4 HG002.pat.chr11.10M.yak HG002.mat.chr11.10M.yak HG002.chr11.10M.bp.hap1.fa
../yak trioeval -t4 HG002.pat.chr11.10M.yak HG002.mat.chr11.10M.yak HG002.chr11.10M.bp.hap2.fa

../yak trioeval -t4 HG002.pat.chr11.10M.yak HG002.mat.chr11.10M.yak HG002.chr11.10M.trio.hap1.fa
../yak trioeval -t4 HG002.pat.chr11.10M.yak HG002.mat.chr11.10M.yak HG002.chr11.10M.trio.hap2.fa

../yak trioeval -t4 HG002.pat.chr11.10M.yak HG002.mat.chr11.10M.yak HG002.chr11.10M.hic.hap1.fa
../yak trioeval -t4 HG002.pat.chr11.10M.yak HG002.mat.chr11.10M.yak HG002.chr11.10M.hic.hap2.fa

5. Let's assemble with HiFi, UL and trio reads

cd /workspace/bin/HiFi_UL_trio

/usr/bin/time -v ../hifiasm -o HG002.chr11.10M.UL.trio -t4 -1 HG002.pat.chr11.10M.yak -2 HG002.mat.chr11.10M.yak --ul ../HG002.UL.chr11.10M.fastq.gz ../HG002.HiFi.chr11.10M.fastq.gz &>>trio.asm.log

6. Let's assemble with HiFi, UL and Hi-C reads

cd /workspace/bin/HiFi_UL_hic

/usr/bin/time -v ../hifiasm -o HG002.chr11.10M.UL.hic -t4 --h1 ../HG002.HiC.chr11.10M.R1.fastq.gz --h2 ../HG002.HiC.chr11.10M.R2.fastq.gz --ul ../HG002.UL.chr11.10M.fastq.gz ../HG002.HiFi.chr11.10M.fastq.gz &>>hic.asm.log