REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
Bama miniature assembly	Zhang et al., 201986	ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/007/644/095/GCA_007644095.1_ASM764409v1
Bama miniature sequencing reads	Zhang et al., 201986	ftp.sra.ebi.ac.uk/vol1/fastq
10 ONT sequencing reads	This paper	Genome Sequence Archive (https://ngdc.cncb.ac.cn/): PRJCA005901
Software and algorithms
Bcftools v1.10.2	Danecek et al., 202187	https://github.com/samtools/bcftools
Bedtools v2.30.0	Quinlan and Hall, 201088	https://github.com/arq5x/bedtools2
BUSCO v3.1.0	Seppey et al., 201989	https://busco.ezlab.org/
BWA v0.7.17-r1188	Li and Durbin, 200990	https://github.com/lh3/bwa
Canu v1.5	Koren et al., 201791	https://github.com/marbl/canu
ClusterProfiler	Yu et al., 201292	https://github.com/GuangchuangYu/clusterProfiler
g:Profile	Raudvere et al., 201993	https://biit.cs.ut.ee/gprofiler/gost
GATK v3.7	McKenna et al., 201094	https://github.com/broadinstitute/gatk
gfatools v0.4-r165	–	https://github.com/lh3/gfatools
GfaViz v1.0.0	Gonnella et al., 201995	https://github.com/ggonnella/gfaviz
Guppy v1.5	Nanopore	https://community.nanoporetech.com/
Minigraph toolkit v0.10-r356	Li et al., 202033	https://github.com/lh3/minigraph
NGMLR v0.2.7	Sedlazeck et al., 201835	https://github.com/philres/ngmlr
Paragraph v2.4a	Chen et al., 201978	https://github.com/Illumina/paragraph
Pilon v1.22	Walker et al., 201496	https://github.com/broadinstitute/pilon
Racon v1.4.6	Vaser et al., 201797	https://github.com/lbcb-sci/racon
RepeatMasker v4.1.4	Tempel, 201298	https://www.repeatmasker.org/
SAMTools v1.9	Li et al., 200999	https://github.com/samtools/samtools
Sniffles v1.0.11	Sedlazeck et al., 201835	https://github.com/fritzsedlazeck/Sniffles
SURVIVOR v1.0.6	Jeffares et al., 2017100	https://github.com/fritzsedlazeck/SURVIVOR
VCFtools v0.1.16	Danecek et al., 2011101	https://github.com/vcftools/vcftools
VEP release 100	McLaren et al., 2016102	https://github.com/Ensembl/ensembl-vep
wtdbg2 v2.5	Ruan and Li, 2020103	https://github.com/ruanjue/wtdbg2