Imperial eagle genome assembly

To generate an imperial eagle genome assembly, we conducted one lane of paired-end (PE) sequencing and one lane of mate-paired (MP) sequencing using an Illumina HiSeq2500 that produced read lengths of 100 bp. We used Trimmomatic 0.35 to remove adaptors and discard low quality bases as in Doyle et al. (2018). We then used ABySS 1.5.2 to conduct several preliminary assemblies of PE and MP reads, using k-mer lengths ranging from 41 to 61. MP reads were used only during the scaffolding step and a minimum of 10 pairs of reads were required to join two contigs. We determined that a k-mer length of 61 produced the best assembly by considering both N50 values and the length of the longest scaffold.