Kang Hu

I've downloaded the gene file (GCF_000004555.2_CB4_rna.fna) for Caenorhabditis briggsae from NCBI and provided the repeat database (cbrrep.ref) sourced from Repbase. However, even after running for some time, the program remains...

Hi @sestaton , My machine supports a maximum of 40 threads. I noticed that when I set a large thread number, for example, 35, Tephra tends to get stuck. Therefore,...

Thank you for your assistance. The program's input and output data are stored in the /home/huk/tephra_lib/rice directory, and there is still sufficient space.  Download links for input data: -...

By the way, when I run the Arabidopsis thaliana genome with the same configuration (20 threads), the same issue occurs as with Caenorhabditis briggsae. The program still gets stuck at...

Hi @oushujun, Should the line `$trf=0 if /^-trf$/i and $ARGV[$k+1]!~/^-/;` be changed to `$trf=$ARGV[$k+1] if /^-trf$/i and $ARGV[$k+1]!~/^-/;` in cleanup.pl? I noticed that when specifying perl ./bin/cleanup.pl -trf 1, the...

Hi @haoyongchao , Thank you for using HiTE. While it is possible to run HiTE on the entire genome or on individual chromosomes separately, I recommend running HiTE on the...

Hi @wjq1981, Thank you for using HiTE, and I apologize for the long runtime. Previously, I didn’t recommend splitting contigs because I was concerned it might break the TE sequences....

Hello @haoyongchao and @wjq1981, I hope you’re well. We’ve noticed that the current version of HiTE might not be ideal for handling large genomes, as it tends to require extensive...

Hi @xiekunwhy, Yes, that's possible. However, I suggest dividing the segments into slightly larger parts, such as 200M or 400M. After merging, you can cluster and remove redundancies across different...

Hi @wjq1981, In HiTE v3.3.1, we’ve replaced LTR_retriever with our newly developed tool, FiLTR, which offers more accurate detection of LTR-RTs. Additionally, we’ve introduced panHiTE, a Nextflow-based tool designed to...