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Related Experiment Video

Updated: Mar 8, 2026

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

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Genome-wide functional analysis using the barcode sequence alignment and statistical analysis (Barcas) tool.

Jihyeob Mun^1,2, Dong-Uk Kim^2,3, Kwang-Lae Hoe⁴

¹Korea Research Institute of Bioscience and Biotechnology (KRIBB), Personalized Genomic Medicine Research Center, Daejeon, Republic of Korea.

BMC Bioinformatics

|February 4, 2017

Summary

Barcas is a new program for analyzing pooled library sequencing data. It accurately maps barcodes and identifies erroneous ones, improving genome-wide functional studies.

Keywords:

Barcode sequencing Barcoded yeast deletion strains Pooled library screen analysis Trie data structure based imperfect matching algorithm sgRNA shRNA

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Published on: June 28, 2018

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Pooled library screens using shRNAs or CRISPR-Cas9 are powerful for genome-wide functional studies.
Barcode production errors can compromise the accuracy of pooled library screens.
Existing tools lack methods to differentiate erroneous barcodes from PCR or sequencing errors during data preprocessing.

Purpose of the Study:

To develop a computational tool for accurate mapping and quality control of barcode sequencing data.
To address the challenge of erroneous barcodes in pooled library screens.
To provide a comprehensive solution for analyzing multiplexed barcode sequencing data.

Main Methods:

Developed the Barcas program, a specialized tool for barcode sequencing (barcode-seq) data analysis.
Implemented a trie data structure-based imperfect matching algorithm for efficient and precise barcode mapping, accommodating mismatches, shifts, and indels.
Integrated functions for barcode library quality control (QC) and distinguishing erroneous barcodes from technical errors.

Main Results:

Barcas enables fast and accurate mapping of barcode sequencing data, handling various sequence variations.
The program effectively identifies and filters erroneous barcodes, enhancing data reliability.
Barcas provides essential quality control metrics for barcode libraries.

Conclusions:

Barcas is a comprehensive, all-in-one package for genome-wide pooled screens.
It offers integrated functions for mapping, data QC, library QC, statistical analysis, and visualization.
This tool improves the accuracy and reliability of pooled library screen analyses.