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Tue Sep 10 20:35:41 2019 UTC (4 years ago) by aloraine
File size: 1516 byte(s)
IGBF-1915 - Add water flea (Daphnia) genomes
1 aloraine 108 <html>
2     <body>
3     <h1>Daphnia magna (Apr 2010) water flea (Xinb3 v2.4) 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_Apr_2010.2bit contains sequence data from <a href="ftp://ftp.ensemblgenomes.org/pub/metazoa/release-44/fasta/daphnia_magna/dna/Daphnia_magna.daphmag2.4.dna.toplevel.fa.gz">ftp://ftp.ensemblgenomes.org/pub/metazoa/release-44/fasta/daphnia_magna/dna/Daphnia_magna.daphmag2.4.dna.toplevel.fa.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_Apr_2010.2bit 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_Apr_2010.bed.gz contains gene models obtained from <a href="ftp://ftp.ensemblgenomes.org/pub/metazoa/release-44/gff3/daphnia_magna/Daphnia_magna.daphmag2.4.44.gff3.gz">ftp://ftp.ensemblgenomes.org/pub/metazoa/release-44/gff3/daphnia_magna/Daphnia_magna.daphmag2.4.44.gff3.gz</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/15752432">wFleaBase: the Daphnia genome database</a>
19     </p>
20     </body>
21     </html>

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