Software Listing of Author : "Dna.engr.uconn.edu"
- IsoEM
- License: Freeware
- Price: 0.00


The IsoEM package can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data. IsoEM uses a novel expectation-maximization algorithm that exploits read disambiguation information provided by the distribution of insert sizes generated during sequencing library preparation, and takes advantage of base quality scores, strand, and read pairing information (if available). Empirical experiments on synthetic datasets show that the algorithm significantly outperforms existing methods of isoform and gene expression level estimation from RNA-Seq data, for details see our AMB paper.
- Publisher: dna.engr.uconn.edu
- Date Released:
- Download Size: 3409 KB
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- Platform: WinOther
- NGSTools
- License: Shareware
- Price:


The NGSTools package provides an object model to enable different types of analyses of Next Generation Sequencing (NGS) data, and some utility programs to process reads aligned to different reference genomes. The most important tools in this package are SNVQ, an accurate Single Nucleotide Variants (SNV) detection and genotyping algorithm from base calls and quality scores and a rule set to merge read alignments to a CCDS transcripts library with alignments of the same reads to a reference assembly. The format of choice to process alignments in every tool in this package is SAM, which allows to integrate NGSTools with commonly used mapping programs as Bowtie and other analysis packages like SAMTools
- Publisher: dna.engr.uconn.edu
- Date Released:
- Download Size: 81 KB
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- Platform: WinOther