BioDemultiplexer is a Julia package designed for demultiplexing reads based on barcodes. It efficiently classifies sequences from FASTQ files, making it a valuable tool in bioinformatics workflows.
The primary function of this package is execute_demultiplexing(). It classifies sequences in an R2 FASTQ file by calculating similarity scores from R1 sequences and barcodes in a reference file. Usage is as follows:
execute_demultiplexing(file_R1, file_R2, bc_file, output_dir)Arguments
file_R1::String: Path to the input R1 FASTQ file.file_R2::String: Path to the input R2 FASTQ file.bc_file::String: Path to the reference barcode file in TSV format.output_dir::String: Path to the directory where demultiplexed files will be saved.
Optional Arguments
max_error_rate::Float64 = 0.22: Maximum permissible error rate for sequence assignment.min_delta::Float64 = 0.1: Minimum difference between the highest and second-highest barcode similarity scores.classify_both::Bool = false: Set to true to classify both R1 and R2 sequences.bc_rev::Bool = true: Set to true to reverse the barcode for demultiplexing.
Demultiplexing can also be performed with a single FASTQ file:
execute_demultiplexing(file_R1, bc_file, output_dir)BioDemultiplexer supports parallel computing, allowing faster processing of large datasets:
using Distributed
addprocs(n)# 'n' is the number of desired workers.
@everywhere using BioDemultiplexer
execute_demultiplexing(file_R1, file_R2, bc_file, output_dir)This package is licensed under the MIT License.