/[genomes]/quickload/D_pulex_Sep_2016/HEADER.md
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Tue Sep 10 20:35:41 2019 UTC (12 months, 2 weeks ago) by aloraine
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IGBF-1915 - Add water flea (Daphnia) genomes
1 aloraine 108 <html>
2     <body>
3     <h1>Daphnia pulex (Sep 2016) water flea (PA42 v3.0) 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_pulex_Sep_2016.2bit contains sequence data from <a href="https://sra-download.ncbi.nlm.nih.gov/traces/wgs03/wgs_aux/FL/TH/FLTH01/FLTH01.1.fsa_nt.gz">https://sra-download.ncbi.nlm.nih.gov/traces/wgs03/wgs_aux/FL/TH/FLTH01/FLTH01.1.fsa_nt.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_pulex_Sep_2016.2bit 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_pulex_Sep_2016.bed.gz contains gene models obtained from <a href="https://www.g3journal.org/highwire/filestream/483384/field_highwire_adjunct_files/3/File_S3.zip">https://www.g3journal.org/highwire/filestream/483384/field_highwire_adjunct_files/3/File_S3.zip</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/28235826">A New Reference Genome Assembly for the Microcrustacean Daphnia pulex</a>
19     </p>
20     </body>
21     </html>

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