FastQC is a quality control tool used to analyze high-throughput sequencing data. It provides detailed graphs and reports that help assess the quality of the data before further downstream analysis.

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Tophat

IGV, and free reads map visualization

transdecoder for translate your mRNA to protein

Samtools

Trimmomatic is a java tool for cut and filter reads

sratools for manage SRA Files

Entrez Direct: E-utilities on the UNIX Command Line

Atom install, packages install. Some awesome packages for atom