High-throughput sequencing alignments

Bowtie
Bowtie 2


Reference based RNA-Seq assembly

Cufflinks

De novo RNA-Seq assembly

Trinity

RNA-Seq quantification

eXpress
Cufflinks


Visualization

IGV Browser (local)
Savant Genome Broswer (local)
UCSC Genome Browser (web only)


Misc

FileZilla
  • Cross platform application to download and upload from a server using SSH or FTP