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Revision 108 - (show annotations)
Tue Sep 10 20:35:41 2019 UTC (4 years, 10 months ago) by aloraine
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IGBF-1915 - Add water flea (Daphnia) genomes
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2 <body>
3 <h1>Daphnia magna (Jan 2019) water flea (SK v1.0) genome assembly</h1>
4 <p>
5 The files listed below are formatted for visualization in the Integrated Genome Browser, available from <a href="https://bioviz.org">BioViz.org</a>.
6 </p>
7 <p>
8 The file named D_magna_Jan_2019.2bit contains sequence data from <a href="ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/990/815/GCA_003990815.1_ASM399081v1/GCA_003990815.1_ASM399081v1_genomic.fna.gz">ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/990/815/GCA_003990815.1_ASM399081v1/GCA_003990815.1_ASM399081v1_genomic.fna.gz</a>. To convert a .2bit to fasta, use twoBitToFa. The file
9 <a href="genome.txt">genome.txt</a> lists sequences and their sizes and was made from
10 D_magna_Jan_2019.2bit sequence file using twoBitInfo. Both twoBitInfo and twoBitToFa are
11 available from <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
12 </p>
13 <p>
14 The file named D_magna_Jan_2019.bed.gz contains gene models obtained from <a href="http://rotifer.skku.edu:8080/Dm_genome_v1.0.gff">http://rotifer.skku.edu:8080/Dm_genome_v1.0.gff</a>. Files with extension .gz were compressed and indexed using bgzip and
15 tabix tools from <a href="https://www.htslib.org">htslib.org</a>.
16 </p>
17 <p>
18 Data associated with paper: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30826642">The genome of the freshwater water flea Daphnia magna: A potential use for freshwater molecular ecotoxicology</a>
19 </p>
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