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