/[genomes]/quickload/D_dama_Nov_2023/HEADER.md
ViewVC logotype

Diff of /quickload/D_dama_Nov_2023/HEADER.md

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 225 by pkulzer, Thu Jan 23 16:23:52 2025 UTC revision 226 by aloraine, Thu Mar 13 19:26:39 2025 UTC
# Line 1  Line 1 
1  <html>  <html>
2  <body>  <body>
3  <h1>Dama dama (Nov 2023) Fallow deer (ASM3311817v1) genome assembly</h1>  <h1>Dama dama (Nov 2023) Fallow deer (ASM3311817v1)</h1>
4  <p>  <p>
5  The files listed below are formatted for visualization in the Integrated Genome  The files listed below are formatted for visualization in the Integrated Genome
6  Browser, available from <a href="https://bioviz.org">BioViz.org</a>.  Browser, available from <a href="https://bioviz.org">BioViz.org</a>.
7  </p>  </p>
8  <p>  <p>
9  Annotation features (gff) files were downloaded from NCBI Genome (<a href="ncbi.nlm.nih.gov/datasets/genome/">ncbi.nlm.nih.gov/datasets/genome/</a>). See the <a href="annots.xml">annots.xml</a> meta-data file in this directory for details.  The "bed.gz" format file contains gene models from a GFF-format file downloaded from the NCBI Genomes Web page for <a href="https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_033118175.1/">Genome assembly ASM3311817v1</a>.
 </p>  
 <p>  
 Files with extension .gz were compressed and indexed using bgzip and  
 tabix tools from <a href="https://www.htslib.org">htslib.org</a>.  
 </p>  
 <p>  
 The file named D_dama_Nov_2023.2bit contains sequence data. It was originally downloaded in fasta format from NCBI Genome and then converted to 2bit by running the faToTwoBit program provided by UCSC. The file <a href="genome.txt">genome.txt</a> lists sequences and their sizes. It was made from the D_dama_Nov_2023.2bit sequence file using the twoBitInfo program.  
 </p>  
 <p>  
 Both twoBitInfo and faToTwoBit are available from <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.  
 </p>  
 <p>  
 More information about this genome assembly and its gene models can be found in the following publication: <a href="https://doi.org/10.1016/j.fsiae.2023.100074">https://doi.org/10.1016/j.fsiae.2023.100074</a>.  
10  </p>  </p>
11  </body>  </body>
12  </html>  </html>
Legend:
Removed from v.225  
changed lines
  Added in v.226
  ViewVC Help
Powered by ViewVC 1.1.26