2.2 Sequence data processing
To ensure comparability between selected studies, we retrieved raw sequencing reads from the SRA run selector and mapped them all to the same Acropora millepora reference genome (Fuller et al., 2020). We used cutadapt to perform adapter trimming and BOWTIE2 to map to our reference genome (Martin, 2011; Langmead & Salzberg, 2012; Langmead et al., 2018). After alignment, we concatenated sequence runs that had coral clones or genotyping replicates, and then used ANGSD to assess the quality of reads for each run (Korneliussen et al., 2014). Detailed script for data processing is maintained on GitHub: https://github.com/SGBes/coral-adaptive-response-to-env-gradients