Input should be completed long-read assemblies in FASTA format, such as those from
CANU
or
HGAP.
Usage
% berokka --outdir trimdir canu.contigs.fasta
<snip>
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 <FASTA> 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 is a brand of effervescent drink and vitamin tablets containing vitamin B and C.
It is a popular cure for a 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
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. Please try that first!
You should only try Berokka if:
NOTE: orientation to dnaA or rep genes is not yet implemented.
Installation
Homebrew
Using Homebrew will install all the dependencies for you: Linux or MacOS
Conda
Using Bioconda) will take care of everything:
Source
You will need to install all the dependencies manually:
Bio::SeqIOandBio::SearchIO)blastn)Usage
Input
Input should be completed long-read assemblies in FASTA format, such as those from CANU or HGAP.
Usage
Output
The
02.trimmed.faoutput has been augmented with new header data (unless--noannoused):circular=true- inform that this is a circular sequence (Rebaler uses this)overhang=N- informs that N bp were trimmed offlen=N- the new contig length if it was present (Canu adds this)suggestCircular=yesif thenoversion was present (Canu adds this)class=repliconif theclass=contigwas present and we circularisedOptions
--filter <FASTA>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 LENGTHcan be used for datasets that won’t seem to circularise. It affects the length of the match it attempts to make using BLAST.--noannowill ensure that the FASTA descriptions are not altered between the input and output FASTA files.--keepfilesand--debugare primarily for use by the developer.Etymology
Berocca is a brand of effervescent drink and vitamin tablets containing vitamin B and C. It is a popular cure for a hangover. A key role of the
berokkatool 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
License
GPLv3
Citation
Not published yet.
Authors