quickload/D_magna_Jan_2019/HEADER.md

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<h1>Daphnia magna (Jan 2019) water flea (SK v1.0) genome assembly</h1>
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The files listed below are formatted for visualization in the Integrated Genome Browser, available from <a href="https://bioviz.org">BioViz.org</a>.
</p>
<p>
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
<a href="genome.txt">genome.txt</a> lists sequences and their sizes and was made from 
D_magna_Jan_2019.2bit sequence file using twoBitInfo. Both twoBitInfo and twoBitToFa are
available from <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
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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
tabix tools from <a href="https://www.htslib.org">htslib.org</a>. 
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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>
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1	<html>
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>
20	</body>
21	</html>