Telomere-to-telomere gap-free genome assembly of horseradish

Codes

All the codes in the genome analysis could be found in the code.txt.

The T2T genome files could be found below in T2T/ and Also Figshare

Figshare: Shen, Fei (2023): Horseradish genome. figshare. Media. https://doi.org/10.6084/m9.figshare.21780176.v2

T2T/

T2T.pro.fa: protein file

T2T.tran.fa: Transcripts file

T2T.gene.gff: Gene annotation gff

T2T.intactTE.gff: intact TE gff

T2T.TEanno.gff: all the annotation TE in the genome

T2T.ncRNA.gff: The non-coding RNA gff

T2T.pro.fa.anno: The interproscan annotation

genome assembly file could be found in Figshare.

LTR-RT analysis/

The important result files in the LTR-RT analysis:

clustered_full_rt.fa: the sequence file of the clustered LTR-RTs

EDTA.pass.list: The result file from EDTA

full_ltr.ltr.acc: The list contain the LTR-RT accession and the other name

full_ltr.ltr.fa: The full-length LTR-RT fasta file

The ONT-based genome assembly could be found in the ONT/

Ar.cds.fa.gz: CDS file

Ar.protein.fa.gz: Protein file

Ar.gene.anno.gz: functional annotation

Ar.gene.gff.gz: Gene models

lg.1013.fa.gz: Genome Fasta

Ar.interproscan.tsv.gz: Interproscan output

all the data could be found in figureshare:

Shen, Fei (2022): horseradish genome. figshare. Dataset. https://doi.org/10.6084/m9.figshare.20003408.v4

Please contact Fei Shen (shenf1028@gmail.com), if you have any question.