ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data
Open Access
- 30 September 2009
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 25 (19), 2607-2608
- https://doi.org/10.1093/bioinformatics/btp450
Abstract
ShortRead is a package for input, quality assessment, manipulation and output of high-throughput sequencing data. ShortRead is provided in the R and Bioconductor environments, allowing ready access to additional facilities for advanced statistical analysis, data transformation, visualization and integration with diverse genomic resources.Keywords
This publication has 9 references indexed in Scilit:
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genomeGenome Biology, 2009
- Design and analysis of ChIP-seq experiments for DNA-binding proteinsNature Biotechnology, 2008
- The UCSC Genome Browser Database: update 2009Nucleic Acids Research, 2008
- Accurate whole human genome sequencing using reversible terminator chemistryNature, 2008
- Mapping short DNA sequencing reads and calling variants using mapping quality scoresGenome Research, 2008
- Mapping and quantifying mammalian transcriptomes by RNA-SeqNature Methods, 2008
- Gene expression profiling by massively parallel sequencingGenome Research, 2007
- ChIP-seq: welcome to the new frontierNature Methods, 2007
- Bioconductor: open software development for computational biology and bioinformaticsGenome Biology, 2004