[HTML][HTML] SAMMate: a GUI tool for processing short read alignments in SAM/BAM format

G Xu, N Deng, Z Zhao, T Judeh, E Flemington… - Source code for biology …, 2011 - Springer
G Xu, N Deng, Z Zhao, T Judeh, E Flemington, D Zhu
Source code for biology and medicine, 2011Springer
Abstract Background Next Generation Sequencing (NGS) technology generates tens of
millions of short reads for each DNA/RNA sample. A key step in NGS data analysis is the
short read alignment of the generated sequences to a reference genome. Although storing
alignment information in the Sequence Alignment/Map (SAM) or Binary SAM (BAM) format is
now standard, biomedical researchers still have difficulty accessing this information. Results
We have developed a Graphical User Interface (GUI) software tool named SAMMate …
Background
Next Generation Sequencing (NGS) technology generates tens of millions of short reads for each DNA/RNA sample. A key step in NGS data analysis is the short read alignment of the generated sequences to a reference genome. Although storing alignment information in the Sequence Alignment/Map (SAM) or Binary SAM (BAM) format is now standard, biomedical researchers still have difficulty accessing this information.
Results
We have developed a Graphical User Interface (GUI) software tool named SAMMate. SAMMate allows biomedical researchers to quickly process SAM/BAM files and is compatible with both single-end and paired-end sequencing technologies. SAMMate also automates some standard procedures in DNA-seq and RNA-seq data analysis. Using either standard or customized annotation files, SAMMate allows users to accurately calculate the short read coverage of genomic intervals. In particular, for RNA-seq data SAMMate can accurately calculate the gene expression abundance scores for customized genomic intervals using short reads originating from both exons and exon-exon junctions. Furthermore, SAMMate can quickly calculate a whole-genome signal map at base-wise resolution allowing researchers to solve an array of bioinformatics problems. Finally, SAMMate can export both a wiggle file for alignment visualization in the UCSC genome browser and an alignment statistics report. The biological impact of these features is demonstrated via several case studies that predict miRNA targets using short read alignment information files.
Conclusions
With just a few mouse clicks, SAMMate will provide biomedical researchers easy access to important alignment information stored in SAM/BAM files. Our software is constantly updated and will greatly facilitate the downstream analysis of NGS data. Both the source code and the GUI executable are freely available under the GNU General Public License at http://sammate.sourceforge.net .
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