nucmer可视化

gitee：https://gitee.com/liaochenlanruo/mummer2circos
github: https://github.com/metagenlab/mummer2circos

来源：https://taylorreiter.github.io/2019-05-11-Visualizing-NUCmer-Output/

比对及R语言可视化

Installing mummer

conda create -n mummer 
conda activate mummer
conda install -c bioconda mummer4=4.0.0beta2

Running nucmer

To download the test data, run:

# M. harundinacea 6AC
wget -O mh6ac.fasta.gz ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/235/565/GCA_000235565.1_ASM23556v1/GCA_000235565.1_ASM23556v1_genomic.fna.gz
gunzip mh6ac.fasta.gz

# M. harundinacea MAG07
wget -O mag07.fasta https://osf.io/d9qyg/download 

The general structure of the nucmer command looks like this:

nucmer --mum reference.fasta query.fasta -p query_ref_nucmer

We will use the genbank assembly as a reference, and the metagenome assembled genome bin as the query.

nucmer --mum mh6ac.fasta mag07.fasta -p m_harundinacea

Here, we filter the nucmer output to only include alignment of length 1000. This is arbitrary, and you should use a length that makes sense for your biological question.

delta-filter -l 1000 -q m_harundinacea.delta > m_harundinacea_filter.delta
show-coords -c -l -L 1000 -r -T m_harundinacea_filter.delta > m_harundinacea_filter_coords.txt

Simple plot

• -r reference fasta
• -q other fasta with to compare with the reference fasta
• -l mendatory option to build circular plots
• genome tracks are ordered based on the order of the input query fasta files

mummer2circos -l -r genomes/NZ_CP008827.fna -q genomes/*fna

nucmer2circos_simple.png

Condensed tracks

mummer2circos -l -c -r genomes/NZ_CP008827.fna -q genomes/*fna

nucmer2circos_condensed.png

With gene tracks

• the header of the reference fasta file chromosome (and eventual plasmids) should be the same as the locus accession of the genbank file. See example file NZ_CP008828.fna.

LOCUS NZ_CP008828 15096 bp DNA CON 16-AUG-2015

mummer2circos -l -r genomes/NZ_CP008827.fna -q genomes/*.fna -gb GCF_000281535_merged.gbk

nucmer2circos_gene_tracks.png

Label specific genes

• given a fasta file of protein of interest, label the BBH of each amino acid sequence on the circular plot
• the fasta headers are used as labels (see example file VF.faa)

mummer2circos -l -r genomes/NZ_CP008827.fna -q genomes/*.fna -gb GCF_000281535_merged.gbk -b VF.faa

nucmer2circos_labels.png

Show mapping depth along the chromosome (and plasmids)

• depth files can be generated from bam file using samtools depth
• the labels used in the .depth file should be the same as the fasta header (see example files)
• regions with depth higher than 2 times the median are croped to that limit and coloured in green (deal with highly repeated sequences).
• regions with depth lower than half of the median depth are coloured in red.

mummer2circos -l -r genomes/NZ_CP008827.fna -q genomes/*.fna -gb GCF_000281535_merged.gbk -b VF.faa -s GCF_000281535.depth

nucmer2circos_depth.png

Add labels based on coordinate file

• structure: LOCUS start stop label (see labels.txt)
• labels can not include spaces

mummer2circos -l -r genomes/NZ_CP008827.fna -q genomes/NZ_FO834906.fna -gb GCF_000281535_merged.gbk -b VF.faa -s GCF_000281535.depth -lf labels.txt

nucmer2circos_labels_coord.png

show links between two genomes

mummer2circos -r genomes/NZ_CP012745.fna -q genomes/*.fna -gb GCF_000281535_merged.gbk -b VF.faa -s GCF_000281535.depth -lf labels.txt

nucmer2circos_links.png