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IGBF-1915 - Add water flea (Daphnia) genomes
| 1 | <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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