10.1093/bioinformatics/btw354 # MultiQC 10.1093/bioinformatics/btv566 # qualimap 10.1093/bioinformatics/bts503 # qualimap 10.1186/1471-2105-12-323 # rsem 10.1093/bioinformatics/bts356 # rseqc 10.1093/bioinformatics/btp352 # Samtools 10.14806/ej.17.1.200 # cutadapt