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https://github.com/metagenlab/mummer2circos

Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments
https://github.com/metagenlab/mummer2circos

Last synced: 4 months ago
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Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments

Host: GitHub
URL: https://github.com/metagenlab/mummer2circos
Owner: metagenlab
License: mit
Created: 2018-01-17T08:38:02.000Z (over 6 years ago)
Default Branch: master
Last Pushed: 2023-12-11T21:01:18.000Z (7 months ago)
Last Synced: 2024-01-17T01:00:39.349Z (6 months ago)
Language: Python
Homepage:
Size: 18.9 MB
Stars: 79
Watchers: 5
Forks: 22
Open Issues: 6
Metadata Files:
- Readme: README.md
- License: LICENSE

Lists

repo-5916-awesome-genome-visualization - mummer2circos - genome-visualization/mummer2circos.png) (Static)
awesome-genome-visualization - mummer2circos

README

[![Downloads](https://anaconda.org/bioconda/mummer2circos/badges/downloads.svg?label=Bioconda)](https://anaconda.org/bioconda/mummer2circos)
[![Anaconda-Server Badge](https://anaconda.org/bioconda/mummer2circos/badges/latest_release_date.svg)](https://anaconda.org/bioconda/mummer2circos)

# 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
conda install -c bioconda -c conda-forge mummer2circos
```

## Method 2: Singularity/Docker container

A docker image is available on DockerHub: [metagenlab/mummer2circos:1.4.2](https://hub.docker.com/layers/metagenlab/mummer2circos/1.4.2/images/sha256-95144bb1e256e7902b417c89ea07679a254602fce2b3f871fc98794284e65b88?context=explore)

### build the image with singularity

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

```bash
singularity build mummer2circos.simg docker://metagenlab/mummer2circos:1.4.2
```

### running with singularity

```bash
singularity exec mummer2circos.simg mummer2circos -r -q -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