GenomicTools is a flexible computational platform for the analysis and manipulation of high-throughput sequencing data such as RNA-seq and ChIP-seq. A variety of mathematical operations between sets of genomic regions is implemented thereby enabling the prototyping of computational pipe...
OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seeding and extension scheme, and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by using very small seeds (12-14 nt), efficiently mapp...
rDiff is an open source tool for accurate detection of differential RNA processing from RNA-Seq data. It implements two statistical tests to detect changes of the RNA processing between two samples. rDiff.parametric is a powerful test, which can be applied for well annotated organisms t...
Strand NGS formerly Avadis NGS is a desktop software platform for alignment, analysis, visualization, and management of data generated by next-generation sequencing (NGS) platforms. It supports workflows for RNA-Seq, DNA-Seq, small RNA-Seq, ChIP-Seq, and Methyl-Seq data analysis. Strand...
BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.
标签：Resequencing, Alignment,Quality Control, RNA-Seq Alignment, Alternative Splicing, Whole Genome Resequencing, SNP discovery,Phylogenetics, Metagenomics,Read Binning
Skewer implements a novel dynamic programming algorithm dedicated to the task of adapter trimming and it is specially designed for processing illumina paired-end sequences.
标签：Small RNA Sequencing, RNA-Seq,Whole Genome Resequencing, De novo Sequencing
The Subread read aligner and Subjunc junction detector employ a novel read mapping paradigm called "seed-and-vote" to achieve a fast mapping speed and a high mapping accuracy. The seed-and-vote paradigm is particularly powerful in detecting indels. Subjunc can be used to discover exon-e...
Samscope is a lightweight SAM/BAM file viewer that makes visually exploring next generation sequencing data as intuitive as Google Maps. Samscope uses multiple layers to simultaneously (or sequentially) view SAM/BAM related features like coverage or allele frequency, or ChIP-SEQ feature...
Search, organize and analyze genomic and protein information of any size via desktop program that provides publication ready images to enhance the impact of your research.
标签：Phylogenetics, Sequence analysis, De-novo assembly,Genomics, Population genetics,Metagenomics, Structural variation, RNA-Seq,Epigenomics
Mapsembler is a targeted assembly software. It takes as input a set of NGS raw reads and a set of input sequences (starters). It first determines if each starter is read-coherent, e.g. whether reads confirm the presence of each starter in the original sequence. Then for each read-cohere...
SOAPfusion is a novel tool for fusion discovery with paired-end RNA-Seq reads. The tool follows a different strategy by “finding fusions directly and verifying them”, differentiating it from all other existing tools by “finding the candidate regions and searching for the fusions afterwa...
Syapse is a platform and application suite for bringing together omics and clinical data.
标签：Allele-specific transcription,DNA methylation, DNA-Seq,InDel discovery, SNP discovery, Structural variation, RNA-Seq, Small RNA transcriptome, ChIP-Seq,Comparative genomics,Comparative transcriptomics,Epigenomics, Genomics,Personal genomics, Population ge