# mummer2circos

**Repository Path**: liaochenlanruo/mummer2circos

## Basic Information

- **Project Name**: mummer2circos
- **Description**: Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments
- **Primary Language**: Unknown
- **License**: Not specified
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 1
- **Forks**: 0
- **Created**: 2022-02-18
- **Last Updated**: 2024-01-03

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# Description

Generate circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments. Generate *SVG* and *PNG* images with circos (http://circos.ca/).

# Installation

## Method 1: Installation with conda


```bash
# create the environment
conda env create -f env.yaml
# activate the environment
conda activate mummer2circos
```

## Method 2: Singularity container   

Dependency: [Singularity](https://sylabs.io/guides/3.0/user-guide/installation.html)

### build the image 

```bash
singularity build mummer2circos.simg docker://metagenlab/mummer2circos:1.2
```

### example

```bash
singularity exec mummer2circos.simg mummer2circos -r <reference.fna> -q <query.fna>  -l
```


# Alignment method

- 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 ...```

# 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

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

![Simple plot](examples/images/nucmer2circos_simple.png)

# Condensed tracks

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

![Simple plot](examples/images/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```

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

![Simple plot](examples/images/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)

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

![Simple plot](examples/images/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.

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

![Simple plot](examples/images/nucmer2circos_depth.png)

# Add labels based on coordinate file

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

```bash
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
```

![Simple plot](examples/images/nucmer2circos_labels_coord.png)

# show links between two genomes 

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

![Simple plot](examples/images/nucmer2circos_links.png)

# Highlight specific ranges based on coordinate file

- overlapping ranges will overlap on the figure
- TODO: add the possibility to input multiple range files that would be displayed on different tracks