FastQC
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Trinity
https://github.com/trinityrnaseq/trinityrnaseq/wiki
IGVtools
https://www.broadinstitute.org/igv/igvtools
FastQC
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Trinity
https://github.com/trinityrnaseq/trinityrnaseq/wiki
IGVtools
https://www.broadinstitute.org/igv/igvtools