Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies.
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TLDR
Btrim is a fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines and can reliably identify barcodes and assign the reads to the original samples.About:
This article is published in Genomics.The article was published on 2011-08-01 and is currently open access. It has received 480 citations till now. The article focuses on the topics: Adapter (computing).read more
Citations
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Journal ArticleDOI
Microbial communities on fish eggs from Acanthopagrus schlegelii and Halichoeres nigrescens at the XuWen coral reef in the Gulf of Tonkin
Shijie Bai,Gang Hou +1 more
TL;DR: The results showed that the microbial communities of coral fish eggs were distinct by species and that key microorganisms were potentially pathogenic, leading to the spoilage of fish eggs, high mortality, and low incubation rates.
Journal ArticleDOI
Read trimming has minimal effect on bacterial SNP-calling accuracy
TL;DR: It was concluded that read quality- and adapter-trimming add relatively little value to a SNP-calling pipeline and may only be necessary if small differences in the absolute number of SNP calls, or the false call rate, are critical.
Book ChapterDOI
MIQE-Compliant Validation of MicroRNA Biomarker Signatures Established by Small RNA Sequencing.
TL;DR: This chapter outlines in detail the material and methods one can apply to reproducibly identify miRNA biomarker signatures from blood total RNA after screening miRNA profiles by small RNA-Seq, resulting data is validated in compliance with the "Minimum Information for Publication of Quantitative Real-Time PCR Experiments" (MIQE) guidelines.
Dissertation
Relationship between the diversity of soil microbial communities and their resistance to different stressors
Posted ContentDOI
GeneQC: A quality control tool for gene expression estimation based on RNA-sequencing reads mapping
TL;DR: A tool called GeneQC (Gene expression Quality Control), which can accurately estimate the reliability of each gene’s expression level, which is designed based on extracted genomic and transcriptomic features and combined using elastic-net regularization and mixture model fitting to provide a clearer picture of mapping uncertainty for each gene.
References
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Journal ArticleDOI
A fast bit-vector algorithm for approximate string matching based on dynamic programming
TL;DR: An algorithm of comparable simplicity that requires only O(kn/w) time by virtue of computing a bit representation of the relocatable dynamic programming matrix for the approximate string matching problem, and is found to be more efficient than the previous results for many choices of k and small.