Key Resource Table.
| REAGENT or RESOURCE |
SOURCE | IDENTIFIER |
|---|---|---|
| Deposited Data | ||
| Silene latifolia female | This study | GWH: PRJCA014197 |
| genome assembly Silene latifolia PacBio | This study | SRA: PRJNA952727 |
| sequences Silene latifolia Hi-C data |
This study | SRA: PRJNA952727 |
| Experimental Models: Organisms/Strains | ||
| Silene latifolia plants | Kazama et al. 80 | Inbred K-line |
| Software and Algorithms | ||
| CCS v6.4 | NA | https://github.com/PacificBiosciences/ccs |
| Hifiasm | Cheng et al.81 | https://github.com/chhylp123/hifiasm |
| ALLHiC V0.9.13 | Zhang et al.50 | https://github.com/tangerzhang/ALLHiC/wiki |
| HiC-Pro | Servant et al.83 | https://github.com/nservant/HiC-Pro |
| BLASTN | Altschul et al.84 | https://blast.ncbi.nlm.nih.gov/Blast.cgi |
| Chromap V0.2.4 | Zhang et al.85 | https://github.com/haowenz/chromap |
| 3D-DNA V180922 | Dudchenko et al.86 | https://github.com/aidenlab/3d-dna |
| Juicebox Assembly Tools | Durand et al.87 | https://github.com/aidenlab/Juicebox |
| HiC Explorer v3.7.2 | Wolff et al.88 | https://hicexplorer.readthedocs.io/en/latest/ |
| BUSCO | Simao et al.89 | https://busco.ezlab.org/ |
| GETA v1.0 | NA | https://github.com/chenlianfu/geta |
| GetaFilter.pl | NA | https://github.com/LengFeng00/biotree.club.git |
| IGV-GSAman | NA | https://gitee.com/CJchen/IGV-sRNA |
| Bowtie | Langmead et al.91 | https://bowtie-bio.sourceforge.net/manual.shtml |
| miRDeep-P | Yang et al.92 | https://github.com/rajewsky-lab/mirdeep2 |
| EDTA v1.9.6 | Ou et al.93 | https://github.com/topics/edta |
| BWA-MEM | Li and Durbin.94 | https://github.com/lh3/bwa |
| Samtools v1.7 | Li et al.95 | https://github.com/samtools/samtools |
| RSEM | Li et al.97 | https://github.com/deweylab/RSEM |
| PAML | Yang et al.99 | http://abacus.gene.ucl.ac.uk/software/paml.html |
| branch model | Yang et al.100 | https://github.com/Bumblebee-Project/Bumblebee/wiki/Branching-Model |