Cited 6 time in
- Genome-wide functional analysis using the barcode sequence alignment and statistical analysis (Barcas) tool
- Jihyeob Mun; Dong Uk Kim; K L Hoe; Seon-Young Kim
- Bibliographic Citation
- BMC Bioinformatics, vol. 17, no. 17S, pp. 475-475
- Publication Year
- Background: Pooled library screen analysis using shRNAs or CRISPR-Cas9 hold great promise to genome-wide functional studies. While pooled library screens are effective tools, erroneous barcodes can potentially be generated during the production of many barcodes. However, no current tools can distinguish erroneous barcodes from PCR or sequencing errors in a data preprocessing step. Results: We developed the Barcas program, a specialized program for the mapping and analysis of multiplexed barcode sequencing (barcode-seq) data. For fast and efficient mapping, Barcas uses a trie data structure based imperfect matching algorithm which generates precise mapping results containing mismatches, shifts, insertions and deletions (indel) in a flexible manner. Barcas provides three functions for quality control (QC) of a barcode library and distinguishes erroneous barcodes from PCR or sequencing errors. It also provides useful functions for data analysis and visualization. Conclusions: Barcas is an all-in-one package providing useful functions including mapping, data QC, library QC, statistical analysis and visualization in genome-wide pooled screens.
- Barcode sequencing; Barcoded yeast deletion strains; Pooled library screen analysis; SgRNA; ShRNA; Trie data structure based imperfect matching algorithm
- Appears in Collections:
- Division of Biomedical Research > Rare Disease Research Center > 1. Journal Articles
Korea Bioinformation Center > 1. Journal Articles
- Files in This Item:
Items in OpenAccess@KRIBB are protected by copyright, with all rights reserved, unless otherwise indicated.