This tool is designed to efficiently split barcodes from sequencing data. It streamlines the preprocessing of genomic data by separating barcodes, enhancing the accuracy of downstream analyses.
Ready to Use After Extraction
This software is designed for ease of use without the need for a complicated installation process. Simply extract the contents of the software package to your preferred location on your system, and it's ready to go.
How to Start:
- Download the
.zipfile. - Extract the contents to a desired location.
- Run the
citrusto start the software.
Single-end barcode splitting
citrus -m 1 -f sample.fq.gz -b barcodes.txt -o output_dir -n sample -e 6 -s 150 -t threads
Paired-end barcode splitting
citrus -m 2 -f sample.fq.gz -b barcodes.txt -o output_dir -n sample -e 6,6 -s 150,50 -t threads
Usage: citrus [OPTIONS] --mode <mode> --fastq <fastq file> --barcode <barcode file> --outdir <output dir> --sample <sample>
Options:
-m, --mode <mode> Set a mode to split barcodes. 1: split the 5' end barcode and conditionally split the 3' end
barcode if identified; 2: split barcodes at both the 5' and 3' ends [possible values: 1, 2]
-f, --fastq <fastq file> Input a fastq file
-b, --barcode <barcode file> Input a barcode file. If there are multiple barcodes in a read, please separate them with a tab
in the input file. When two barcodes complement each other in reverse, only the 5' end barcode
is needed
-q, --testseq <test seq file> Input a test sequence file
-o, --outdir <output dir> Output directory
-n, --sample <sample> Sample name
-e, --err <err threshold> Threshold of Levenshtein Distance value or sequencing error rate. Use a comma to separate two
numbers, when there are different thresholds for the 5' and 3' ends [default: 6]
-s, --shift <shift threshold> Threshold of shift length for identifying barcode sequences. Use a comma to separate two
numbers, when there are different thresholds for the 5' and 3' ends [default: 150,50]
-u, --trim_len <trim len> The length of the 3' end barcode sequence to be trimmed [default: 0]
-c, --seed_size <seed size> Seed size [default: 5]
-d, --step_size <step size> Step size [default: 1]
-t, --thread <thread> Number of threads [default: 4]
-r, --retain Retain barcode sequences on reads
-g, --degenerate Allow degenerate bases in barcodes and primers
-h, --help Print help
-V, --version Print version
The barcode file must contain three tab-separated columns: ID, 5' barcode sequence, and 3' barcode sequence. The ID can be the number of a barcode, or names like sample name, species name, or tissue name, etc. Additionally, one ID can correspond to multiple pairs of barcode sequences.
As shown in the example, if the ID is BC1, the barcode file would be structured as follows:
| BC1 | ATCG | TCAG |
This tool offers two versions:
GNU version (recommended): Faster and more memory-efficient. Requires a recent version(>=2.31) of glibc on your Linux system.
Musl version: Highly portable and compatible with a wider range of Linux systems, including those with older glibc versions.
As shown in the diagram, sequencing data size is 4.66G, with 10 threads.
夏小双 Xiaoshuang Xia ([email protected])
Research Use Only
This software is provided strictly for individual research purposes. Commercial use is strictly prohibited. This means:
Allowed: Personal academic research, personal learning, and non-commercial experimentation.
Not Allowed: Any form of commercial application, distribution, or use that generates revenue directly or indirectly. This includes, but is not limited to, integration into commercial products, offering this software as a service, or using it for commercial gain.
For commercial licensing or permissions, please contact us.