Merqury安装及使用

merqury github

一、安装

conda create -n merqury -c bioconda -c conda-forge merqury
conda activate merqury
Rscript $MERQURY/plot/plot_spectra_cn.R --help
merqury.sh

 

./merqury.sh <read-db.meryl> [<mat.meryl> <pat.meryl>] <asm1.fasta> [asm2.fasta] <out>

Usage: merqury.sh <read-db.meryl> [<mat.meryl> <pat.meryl>] <asm1.fasta> [asm2.fasta] <out>
    <read-db.meryl>    : k-mer counts of the read set
    <mat.meryl>        : k-mer counts of the maternal haplotype (ex. mat.only.meryl or mat.hapmer.meryl)
    <pat.meryl>        : k-mer counts of the paternal haplotype (ex. pat.only.meryl or pat.hapmer.meryl)
    <asm1.fasta>    : Assembly fasta file (ex. pri.fasta, hap1.fasta or maternal.fasta)
    [asm2.fasta]    : Additional fasta file (ex. alt.fasta, hap2.fasta or paternal.fasta)
    *asm1.meryl and asm2.meryl will be generated. Avoid using the same names as the hap-mer dbs
    <out>        : Output prefix

 

二、Example

run Merqury using the prebuilt meryl dbs on a. thaliana F1 hybrid

### Download assemblies ###
wget https://gembox.cbcb.umd.edu/triobinning/athal_COL.fasta
wget https://gembox.cbcb.umd.edu/triobinning/athal_CVI.fasta

### Download prebuilt meryl dbs ###
# read.meryl of the F1 hybrid between COL-0 and CVI-0
wget https://obj.umiacs.umd.edu/marbl_publications/merqury/athal/a_thal.k18.meryl.tar.gz
# hap-mers for COL-0 haplotype
wget https://obj.umiacs.umd.edu/marbl_publications/merqury/athal/a_thal.col0.hapmer.meryl.tar.gz
# hap-mers for CVI-0 haplotype
wget https://obj.umiacs.umd.edu/marbl_publications/merqury/athal/a_thal.cvi0.hapmer.meryl.tar.gz

# Untar
for gz in *.tar.gz
do
    tar -zxf $gz
done

###Run merqury
merqury.sh F1.k18.meryl col0.hapmer.meryl cvi0.hapmer.meryl athal_COL.fasta athal_CVI.fasta test

 

三、QV分析流程

STEP00 Prepare meryl dbs

1、得到合适的k值（当不确定使用多大的kmer时，使用best_k.sh with genome_size in num.of basea。以人类基因组为例，best kmer = 21）

sh $MERQURY/best_k.sh <genome_size> [tolerable_collision_rate=0.001]

2、批量化构建k-mer dbs（以illumina WGS reads为例）

for each read$i.fastq.gz
do
    # 1. Build meryl dbs
    meryl k=$k count output read$i.meryl read$i.fastq.gz
done

# 2. Merge
meryl union-sum output $genome.meryl read*.meryl

STEP01 Run merqury

# 此处应用适用于没有父母本hap-mers的情况（更多使用案例见官网）

merqury.sh read-db.meryl asm1.fasta asm2.fasta out_prefix