RStudio is an integrated development environment (IDE) for R

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

A quality control analysis tool for high throughput sequencing data

Automatically exported from code.google.com/p/figtree

Genome-scale protein function classification

Java tools for analyzing Drop-seq data

csf fork of fastqc for usage on selected reads of unaligned bam file