References

• Bowtie2: Langmead and Salzberg, Fast gapped-read alignment with Bowtie2, Nature Methods (2012).
• STAR: Dobin et al., STAR: ultrafast universal RNA-seq aligner, Bioinformatics (2013).
• Sambamba: Tarasov et al., Sambamba: fast processing of NGS alignment formats, Bioinformatics (2015).
• Sargasso: Qiu et al., Mixed-species RNA-seq for elucidation of non-cell-autonomous control of gene transcription, Nature Protocols (2018).