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
USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST.
Vcfanno provides fast, flexible annotation of genetic variants
Velvet is a de novo genomic assembler specially designed for short read sequencing technologies such as Solexa or 454.
a swiss-army knife of tools for a wide-range of genomics analysis tasks.
Spliced Transcripts Alignment to a Reference
Strelka is an analysis package designed to detect somatic SNVs and small indels from the aligned sequencing reads of matched tumor-normal samples.
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.