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 Genomatix Mining Station (GMS) offers mapping of NGS reads onto genomes, transcriptomes and splice-junction libraries. It is a client-server based solution and can be controlled through an intuitive GUI or via command-line. It covers different tasks such as, as genomic positioning, ...
FluxCapacitor s a computer program to predict splice form abundancies from reads of an RNA-seq experiment. FluxSimulator can generate simulated data for testing RNA-seq pipelines
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...
RobiNA is a Java GUI that enables the user to graphically call differentially expressed genes. For read mapping it relies on bowtie and for the differntial expression analysis it builds on an R backbone running DESeq and edgeR.
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...
CRAC is a mapping software specialized for RNA-Seq data. It detects mutations, indels, splice or fusion junctions in each single read.
We propose a novel way of analyzing reads that integrates genomic locations and local coverage, and delivers all above mentioned predictions in a singl...
标签：Mapping, RNA Seq analysis,RNA-Seq Alignment, Alternative Splicing, Fusion genes, Fusion transcripts, SNP discovery,InDel discovery
Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.
Processes raw sequence data from Sanger or 454 sequencing into a hybrid de-novo assembly, annotates it and produces GMOD compatible output, including a SeqFeature database suitable for GBrowse.
Sensitive peptide detection on noisy matured sequences. A self-training integrative pipeline for predicting CDS in transcripts which can adapt itself to different levels of sequence qualities.