SDAMtools is a set of command-line tools for the manipulation of files containing aligned NGS reads.
The FASTX-Toolkit is a collection of command line tools for NGS FASTA/FASTQ files preprocessing.
Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data using the R statistical programming language
Galaxy is a web genomics toolkit platform that includes many tools for NGS analysis
GenePattern is a powerful genomic analysis platform that provides access to tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks.
eXpress is a streaming tool for quantifying the abundances of a set of target sequences such as transcript-level RNA-Seq quantification
DEGseq is an R package to identify differentially expressed genes from RNA-Seq data
edgeR is an R package to calculate differential expression of RNA-seq gene expression profiles using empirical Bayes estimation and exact tests
Trinity is an efficient method for de novo reconstruction of transcriptomes from RNA-seq data.