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ESTclean: a cleaning tool for next-gen transcriptome shotgun sequencing
- Source :
- BMC Bioinformatics
- Publication Year :
- 2012
- Publisher :
- Springer Science and Business Media LLC, 2012.
-
Abstract
- Background With the advent of next-generation sequencing (NGS) technologies, full cDNA shotgun sequencing has become a major approach in the study of transcriptomes, and several different protocols in 454 sequencing have been invented. As each protocol uses its own short DNA tags or adapters attached to the ends of cDNA fragments for labeling or sequencing, different contaminants may lead to mis-assembly and inaccurate sequence products. Results We have designed and implemented a new program for raw sequence cleaning in a graphical user interface and a batch script. The cleaning process consists of several modules including barcode trimming, sequencing adapter trimming, amplification primer trimming, poly-A tail trimming, vector screening and low quality region trimming. These modules can be combined based on various sequencing applications. Conclusions ESTclean is a software package not only for cleaning cDNA sequences, but also for helping to develop sequencing protocols by providing summary tables and figures for sequencing quality control in a graphical user interface. It outperforms in cleaning read sequences from complicated sequencing protocols which use barcodes and multiple amplification primers.
- Subjects :
- 0106 biological sciences
DNA nanoball sequencing
DNA, Complementary
Sequence assembly
Computational biology
Biology
01 natural sciences
Biochemistry
03 medical and health sciences
Structural Biology
Animals
Molecular Biology
Illumina dye sequencing
DNA Primers
030304 developmental biology
Expressed Sequence Tags
Genetics
Whole genome sequencing
0303 health sciences
Massive parallel sequencing
Shotgun sequencing
Applied Mathematics
High-Throughput Nucleotide Sequencing
Sequence Analysis, DNA
Computer Science Applications
ComputingMethodologies_PATTERNRECOGNITION
Drosophila melanogaster
Single cell sequencing
Transcriptome
Software
ABI Solid Sequencing
010606 plant biology & botany
Subjects
Details
- ISSN :
- 14712105
- Volume :
- 13
- Database :
- OpenAIRE
- Journal :
- BMC Bioinformatics
- Accession number :
- edsair.doi.dedup.....83fc3daa5fdd8527b45166d56cad6b49