TopHat is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions.
Consistent quality and adapter trimming for RRBS or standard FastQ files
Trimmomatic: A flexible read trimming tool for Illumina NGS data
Trinity assembles transcript sequences from Illumina RNA-Seq data.
Twinscan gene-structure prediction
C++ library and its applications to generate and process accurate consensus sequences
SPAdes – St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines
The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
a swiss-army knife of tools for a wide-range of genomics analysis tasks.
Spliced Transcripts Alignment to a Reference
