strapdown: '/styling/strapdown/v/0.2/strapdown.js'}; 
<h1>Banana genome assembly</h1>
<body>

<p> This directory contains annotation and sequence data files from
the banana Musa acuminata DH Pahang version 2 genome assembly released January 2016. Files
are formatted for visualization in <a href="https://bioviz.org/">Integrated Genome Browser</a> (IGB).
</p>

<p>
Files include:
</p>
<p>
<ul>
<li>
2bit file - sequence file in two-bit format, created using
faToTwoBit. 
When users click <b>Load Sequence</b> buttons, IGB retrieves sequence data from this file. The 2bit file name must match the genome version.
To obtain a copy of faToTwoBit, visit <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>. 
</li>
<li>
annots.xml - meta-data file that lists available data sets and specifies how they will look once loaded into <a href="https://bioviz.org">Integrated Genome Browser</a>.

<li>genome.txt - meta-data file listing genomic sequences and their sizes, created using twoBitInfo using the 2bit file. To obtain a copy of twoBitInfo, visit <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>

<li>reference gene model annotations bed detail format, compressed using bgzip and indexed using tabix (See: <a href="http://bioinformatics.oxfordjournals.org/content/27/5/718">Tabix: fast retrieval of sequence features from generic TAB-delimited files</a> and <a href="http://genome.ucsc.edu/FAQ/FAQformat.html">http://genome.ucsc.edu/FAQ/FAQformat.html</a>.)
</ul>
</p>
<p>
<b>Note:</b> Gene model annotation files have been re-formatted for fast transfer over the internet and for visualization in IGB. 
</p>
<p>Gene model annotation file(s) include:
<ul>
<li>M_acuminata_DH_Pahang_Jan_2016.bed.gz - gene models downloaded in GFF3 format from the <a href="http://banana-genome-hub.southgreen.fr/download">Banana Genome Hub download page</a> and converted to IGB-friendly format (BED-detail) using gff3ToBedDetail.py from this <a href="https://bitbucket.org/lorainelab/genomesource">git repository</a>. 
</li>
</ul>
<p>
For more information about quickload, visit <a href="https://bioviz.org">bioviz.org</a> and visit the on-line, searchable IGB User's Guide.
</p>
</body>
[ICO]NameLast modifiedSizeDescription
[PARENTDIR]Parent Directory  -  
[ ]annots.xml2023-06-16 13:49 319 Annotation and data file list
[TXT]genome.txt2023-06-16 13:49 347 Chromosome lengths and assembly information
[ ]M_acuminata_DH_Pahang_Jan_2016.bed.gz.tbi2023-06-16 13:49 165KTabix index file
[ ]M_acuminata_DH_Pahang_Jan_2016.bed.gz2023-06-16 13:49 2.3MAnnotation or junction file
[ ]M_acuminata_DH_Pahang_Jan_2016.2bit2023-06-16 13:49 108MSequence data in blat 2bit format
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