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BC-store: a program for mgiseq barcode sets analysis
- Source :
- PLoS ONE, Vol 16, Iss 3, p e0247532 (2021), PLoS ONE
- Publication Year :
- 2020
- Publisher :
- Cold Spring Harbor Laboratory, 2020.
-
Abstract
- Here we present the devised BC-store–a program for analyzing and selecting sets of barcodes for sequencing on platforms manufactured by MGI Tech (China). The app is available as an open source in Python3 and as a desktop version. The application allows analyzing the compatibility of barcodes on a single lane of a flow cell in a set in the case of equal and arbitrary fractions. In addition, with the help of this tool barcodes can be added to an existing set with custom share options. In this paper we describe how BC-store works for different tasks and consider the effectiveness of using BC-store in sequence lab routine tasks.<br />Author summary The performance of modern NGS machines allows considerable amount of data to be obtained which exceed the data required for one specific sample. To pool multiple samples on a single lane of the flow cell, barcoding is used–adapters carrying a unique nucleotide sequence are introduced by ligation [1]. Adapters are sequenced from their specific primers. Their sequences are used for demultiplexing the sequencing results for individual fastq files by programs like zebracall [2] or bcl2fastq [3]. The task of selecting the adapters for a set is similar to sequencing low diversity libraries [4]: if all adapters on the lane have the same nucleotide during this sequencing cycle, the quality of its reading drops dramatically. Therefore, manufacturers recommend grouping the adapters by sets. However, the sets offered by MGI Tech [5] are far from routine practice, as they do not allow for non-equimolar sample pooling by default, and they have other disadvantages (more on them later in the text). To overcome these problems, we created the BC-store program, which allows analyzing the sets of MGI Tech barcodes entered by the user to be further used in sequencing. This tool also provides the opportunity to vary the number of simultaneously sequenced samples, to use reagents more efficiently, and, as a result, to correctly distribute reads across samples, which helps to increase both the quality of sequencing and the level of data interpretation.
- Subjects :
- Source code
Computer science
computer.software_genre
Barcode
Biochemistry
law.invention
Open Science
law
media_common
0303 health sciences
Sequence
Multidisciplinary
Database
Nucleotides
Applied Mathematics
Simulation and Modeling
030302 biochemistry & molecular biology
Software Engineering
High-Throughput Nucleotide Sequencing
Physical Sciences
Engineering and Technology
Medicine
Data mining
Cellular Structures and Organelles
Open Source Software
Algorithms
Research Article
Computer and Information Sciences
Science Policy
media_common.quotation_subject
Science
Nucleotide sequencing
Nucleotide Sequencing
Research and Analysis Methods
Set (abstract data type)
Computer Software
03 medical and health sciences
DNA Barcoding, Taxonomic
Humans
Molecular Biology Techniques
Sequencing Techniques
Signal to Noise Ratio
Molecular Biology
030304 developmental biology
Base Sequence
Biology and Life Sciences
Open source software
Cell Biology
Source Code
Signal Processing
computer
Mathematics
Software
Subjects
Details
- Database :
- OpenAIRE
- Journal :
- PLoS ONE, Vol 16, Iss 3, p e0247532 (2021), PLoS ONE
- Accession number :
- edsair.doi.dedup.....2ac7fce30d27200c206e43982c4e2d8c