A fast tool to search for barcode sequences inside fasta/fastq data. Can also remove the reads that have a barcode. Internally, uses the Aho-Corasick multiple string matching algorithm implementation from here.
Compile by running make. Compiling requires a C++ compiler with support for the C++17 standard. Tested to work with g++ version 9.
There is some example data provided in the repository. Running barcode analysis on reads at example_data/reads.fastq with barcodes at example_data/barcodes.txt:
./barcode_analyzer analyze -i example_data/reads.fastq -b example_data/barcodes.txt
Filtering reads with barcodes with the same inputs, writing output to example_data/filtered.fastq:
./barcode_analyzer filter -i example_data/reads.fastq -b example_data/barcodes.txt -o example_data/filtered.fastq
There are two commands:
Available commands:
./barcode_analyzer analyze
./barcode_analyzer filter
Running a command without arguments prints the usage instructions for the command.
Search for barcode sequences inside a fasta/fastq file.
Usage:
analyze [OPTION...]
-i arg The sequence file in fasta or fastq format.
-o arg Output file. If not given, prints to stdout.
-b arg A file containing the barcodes, one per line. Do not give
reverse complements.
-v, --verbose Verbose output.
-h, --help Print usage
Remove all sequences from a fasta/fastq file that have a barcode sequence.
Usage:
filter [OPTION...]
-i arg The sequence file in fasta or fastq format.
-o arg Output file.
-b arg A file containing the barcodes, one per line. Do not give
reverse complements.
-h, --help Print usage