EM-SNP is an unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms
PASSion uses the mapped read in a pair as anchor and then uses a high resolution algorithm, pattern growth, to remap the proximal and distal fragments of the unmapped read to a local region of the reference indicated by the mate. It is capable of identifying both known and novel canonical and non-canonical junctions with SNP or sequencing error tolerance.
::DEVELOPER
Yanju Zhang (Leiden University Medical Center, The Netherlands): y.zhang AT lumc.nl
VDJSeq-Solver is a completely automated workflow for the in silico detection of the main clone V(D)J recombination sequence characterizing neoplastic tissues, using RNA-Seq paired-end reads.
IDP is an gene Isoform Detection and Prediction tool from Second Generation Sequencing and PacBio sequencing. It offers very reliable gene isoform identification with high sensitivity.
IDP-fusion is an gene Isoform Detection and Prediction tool from Second Generation Sequencing and PacBio sequencing.
Kin Fai Au, Vittorio Sebastiano, Pegah Tootoonchi Afshar, Jens Durruthy Durruthy, Lawrence Lee, Brian A. Williams, Honoratus Van Bakel, Eric Schadt, Renee A. Reijo Pera, Jason Underwood, Wing Hung Wong Characterization of the human ESC transcriptome by hybrid sequencing
Proc. Natl. Acad. Sci. USA 2013 110 (50) E4821-E4830
The intcomp R package provides a benchmarking tools for quantitative comparison of cancer gene detection algorithms based on integrative analysis of DNA copy number and gene expression data.
NovelSeq is a computational framework to discover the content and location of long novel sequence insertions using paired-end sequencing data generated by the next-generation sequencing platforms. Our framework can be built as part of a general sequence analysis pipeline to discover multiple types of genetic variation (SNPs, structural variation, etc.), thus it requires significantly less-computational resources than de novo sequence assembly. We apply our methods to detect novel sequence insertions in the genome of an anonymous donor and validate our results by comparing with the insertions discovered in the same genome using various sources of sequence data.