Genome-wide functional analysis using the barcode sequence alignment and statistical analysis (Barcas) tool.
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.
Korea Research Institute of Bioscience and Biotechnology (KRIBB), Personalized Genomic Medicine Research Center, Daejeon, Republic of Korea.|Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea.
Jihyeob
J
Mun
Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea.|Korea Research Institute of Bioscience and Biotechnology (KRIBB), Aging Research Center, Daejeon, Republic of Korea.
Dong-Uk
DU
Kim
Graduate School of New Drug Discovery and Development, Chungnam National University, Yusong-gu, Daejeon, South Korea.
Kwang-Lae
KL
Hoe
Korea Research Institute of Bioscience and Biotechnology (KRIBB), Personalized Genomic Medicine Research Center, Daejeon, Republic of Korea. kimsy@kribb.re.kr.|Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea. kimsy@kribb.re.kr.
Seon-Young
SY
Kim
D000465:Algorithms; D000818:Animals; D064113:CRISPR-Cas Systems; D003627:Data Interpretation, Statistical; D016678:Genome; D006801:Humans; D051379:Mice; D034741:RNA, Small Interfering; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D034741:RNA, Small Interfering
Barcode sequencing; Barcoded yeast deletion strains; Pooled library screen analysis; Trie data structure based imperfect matching algorithm; sgRNA; shRNA