Generate circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments. Generate SVG and PNG images with circos (http://circos.ca/).
conda install -c bioconda -c conda-forge mummer2circos
A docker image is available on DockerHub: metagenlab/mummer2circos:1.4.2
singularity build mummer2circos.simg docker://metagenlab/mummer2circos:1.4.2
singularity exec mummer2circos.simg mummer2circos -r <reference.fna> -q <query.fna> -l
- the whole genome alignments can be done with three different methods: megablast, nucmer or promer
- use the parameter -a to indicate which method to use. Nucmer is the default option.
mummer2circos -l -a promer ...
- -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
mummer2circos -l -c -r genomes/NZ_CP008827.fna -q genomes/*fna
- 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
- 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
- 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
- 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
mummer2circos -r genomes/NZ_CP012745.fna -q genomes/*.fna -gb GCF_000281535_merged.gbk -b VF.faa -s GCF_000281535.depth -lf labels.txt
- overlapping ranges will overlap on the figure
- TODO: add the possibility to input multiple range files that would be displayed on different tracks