Assembly of the T. ichikawai genome
A scaffold-level assembly of the T. ichikawai genome was
generated under the stLFR2Supernova pipeline (Wang et al., 2019) with
Supernova 2.1.1 (Weisenfeld et al., 2017). Parameters for the Supernova
run were set to MAX_READS = 400000000 and MINSIZE = 200. The assembly
was polished automatically with the Pilon software tool (Walker et al.,
2014). The quality of the genome assembly was evaluated using the
completeness estimated by BUSCO version 5.4.4 (Simão et al., 2015)
with a database of ray-finned
fishes (Actinopterygii odb10). Transposable elements (TEs) and other
repeat sequences of the T. ichikawai genome were identified using
RepeatModeler version 2.0.3 (Flynn et al., 2020) with Dfam 3.7 repeat
database. Second, the TEs and repeats within the T. ichikawaigenome were soft-masked by RepeatMasker version 4.1.2-p1
(http://www.repeatmasker.org).