PRADA : Pipeline for RNA-Sequencing Data Analysis
SOLiD Assembler TRAnslation Program
Integrative proteogenomics beyond six-frames and SNPs
Highly-accurate de novo assembler of paired-end RNA-Seq
Blast query sequences on a set of fasta formatted genomes
A visualization and analysis tool of Bacterial NGS data for Biologists
RNA-Seq analysis pipeline for QC, Expression, DifferentialExpression
Rapid gRNA design and validation for CRISPR
A tool for transcript identification and quantification with RNA-Seq
Program to identify Variants Associated with Aberrant Splicing
Analyze time-course data with significance tests, clustering, modeling
ChIP-seq analysis tool
QC for variant discovery from next gen sequence in pedigrees
Seq: Gestore di processi sequenziali con esecuzione da smartphone
RNA-Seq driven gene finding incorporating ambiguous reads
ChIP-seq data pre-processing software
Bycom can do methylcytosine calling (5mC calling) from BS-seq.
snpSniffer is a sample integrity checking tool for NGS data
Enhanced splice junction detection and estimation from RNA-Seq data
This software identifies tag-enriched regions(hotspots) from DNase-seq
ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq