https://github.com/tseemann/berokka
🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
https://github.com/tseemann/berokka
bioinformatics circular-genome genome-assembly genomics long-read-sequencing
Last synced: 6 months ago
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🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
- Host: GitHub
- URL: https://github.com/tseemann/berokka
- Owner: tseemann
- License: gpl-3.0
- Created: 2016-10-13T07:30:17.000Z (almost 9 years ago)
- Default Branch: master
- Last Pushed: 2019-09-07T07:03:54.000Z (about 6 years ago)
- Last Synced: 2024-06-13T00:03:07.815Z (over 1 year ago)
- Topics: bioinformatics, circular-genome, genome-assembly, genomics, long-read-sequencing
- Language: Perl
- Homepage:
- Size: 3.51 MB
- Stars: 25
- Watchers: 4
- Forks: 3
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
[](https://travis-ci.org/tseemann/berokka)
[](https://www.gnu.org/licenses/gpl-3.0)
# berokka
Trim, circularise, orient & filter long read bacterial genome assemblies
## Introduction
There is already a good piece of software to trim/circularise and orient
genome assemblies called [Circlator](https://sanger-pathogens.github.io/circlator/).
Please try that first!
You should only try Berokka if:
1. You only have the contig files and do not have the corrected reads anymore
2. Your contigs are simple cases with clear overhang and could be done manually with BLAST
3. Circlator fails on your data even after [troubleshooting](https://github.com/sanger-pathogens/circlator/wiki/Troubleshooting)
**NOTE:** orientation to *dnaA* or *rep* genes is not yet implemented.
## Installation
### Homebrew
Using Homebrew will install all the dependencies for you:
[Linux](http://linuxbrew.sh) or [MacOS](http://brew.sh)
```
brew install brewsci/bio/berokka
```
### Conda
Using [Bioconda](https://bioconda.github.io/user/install.html#install-conda))
will take care of everything:
```
conda install -c conda-forge -c bioconda -c defaults berokka
```
### Source
```
git clone https://github.com/tseemann/berokka.git
./berokka/bin/berokka -h
```
You will need to install all the dependencies manually:
* [BioPerl](http://bioperl.org/) >= 1.6 (for `Bio::SeqIO` and `Bio::SearchIO`)
* [BLAST+](ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/) >= 2.3.0 (for `blastn`)
## Usage
### Input
Input should be completed long-read assemblies in FASTA format, such as those from
[CANU](https://github.com/marbl/canu)
or
[HGAP](https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/HGAP-in-SMRT-Analysis).
### Usage
```
% berokka --outdir trimdir canu.contigs.fasta
Did you know? berokka is a play on the concept of overhang vs hangover
% ls trimdir/
01.input.fa
02.trimmed.fa
03.results.tab
% cat trimdir/03.results.tab
#sequence status old_len new_len trimmed
tig00000000 trimmed 5461026 5448790 12236
tig00000002 trimmed 138825 113601 25224
tig00000003 trimmed 57075 43297 13778
tig00000004 kept 24900 24900 0
tig00000006 trimmed 1620 1320 300
tig00000007 removed 2380 0 0
```
### Output
Filename | Format | Description
---------|--------|--------------
01.input.fa | FASTA | All the input sequences
02.trimmed.fa | FASTA | The (possibly) trimmed sequences
03.results.tab | TSV | Summary of results
The `02.trimmed.fa` output has been augmented with new header data (unless `--noanno` used):
* `circular=true` - inform that this is a circular sequence (Rebaler uses this)
* `overhang=N` - informs that N bp were trimmed off
* `len=N` - the new contig length if it was present (Canu adds this)
* `suggestCircular=yes` if the `no` version was present (Canu adds this)
* `class=replicon` if the `class=contig` was present *and* we circularised
### Options
* `--filter ` allows you to remove contigs which match 50% of sequences in this file.
Berokka comes with the standard Pacbio control sequence. You can provide your own FASTA file
using this option. If you want to disable filtering, use `--filter 0`.
* `--readlen LENGTH` can be used for datasets that won't seem to circularise.
It affects the length of the match it attempts to make using BLAST.
* `--noanno` will ensure that the FASTA descriptions are not altered between the input
and output FASTA files.
* `--keepfiles` and `--debug` are primarily for use by the developer.
## Etymology
[Berocca](https://en.wikipedia.org/wiki/Berocca) is a brand of effervescent drink and vitamin tablets containing vitamin B and C.
It is a popular cure for a [hangover](https://en.wikipedia.org/wiki/Hangover). A key role of the `berokka` tool is to remove the
"overhang" that occurs at the ends of long-read assemblies of circular genomes.
## Feedback
Please file questions, bugs or ideas to the [Issue Tracker](https://github.com/tseemann/berokka/issues)
## License
[GPLv3](https://raw.githubusercontent.com/tseemann/berokka/master/LICENSE)
## Citation
Not published yet.
## Authors
* Torsten Seemann