TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches

Table 1 Comparison of the TE insertion/deletion detection efficiency by TrEMOLO using genome assemblies of different quality

Assembly process	Contigs/scaffolds number	N50 (bp)	BUSCO	Assembly total size (bp)	Number of TE insertions	Number of INSIDER TE insertions	Number of OUTSIDER TE insertions	Number of INSIDER TE deletions
Flye + Racon (4 runs) + Ragoo^a	30	27,282,734	98%	148,869,489	2334	60	2274	49
Flye + Racon (1 run) + Ragoo^a	31	27,316,827	96.9%	149,145,078	2339	54	2285	49
Shasta + Ragoo^a	15	27,256,021	93%	151,203,880	2344	94	2250	56
Wtdbg2 + Ragoo^a	22	34,296,233	92.6%	171,989,387	2579	159	2420	109

ISSN: 1474-760X