Banana genome assembly

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 Integrated Genome Browser (IGB).

Files include:

• 2bit file - sequence file in two-bit format, created using faToTwoBit. When users click Load Sequence buttons, IGB retrieves sequence data from this file. The 2bit file name must match the genome version. To obtain a copy of faToTwoBit, visit http://hgdownload.cse.ucsc.edu/admin/exe/.
• annots.xml - meta-data file that lists available data sets and specifies how they will look once loaded into Integrated Genome Browser.
• 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 http://hgdownload.cse.ucsc.edu/admin/exe/
• reference gene model annotations bed detail format, compressed using bgzip and indexed using tabix (See: Tabix: fast retrieval of sequence features from generic TAB-delimited files and http://genome.ucsc.edu/FAQ/FAQformat.html.)

Note: Gene model annotation files have been re-formatted for fast transfer over the internet and for visualization in IGB.

Gene model annotation file(s) include:

• M_acuminata_DH_Pahang_Jan_2016.bed.gz - gene models downloaded in GFF3 format from the Banana Genome Hub download page and converted to IGB-friendly format (BED-detail) using gff3ToBedDetail.py from this git repository.

For more information about quickload, visit bioviz.org and visit the on-line, searchable IGB User's Guide.

	Name	Last modified	Size	Description
	Parent Directory		-
	M_acuminata_DH_Pahang_Jan_2016.2bit	2023-06-16 13:49	108M	Sequence data in blat 2bit format
	M_acuminata_DH_Pahang_Jan_2016.bed.gz	2023-06-16 13:49	2.3M	Annotation or junction file
	M_acuminata_DH_Pahang_Jan_2016.bed.gz.tbi	2023-06-16 13:49	165K	Tabix index file
	annots.xml	2023-06-16 13:49	319	Annotation and data file list
	genome.txt	2023-06-16 13:49	347	Chromosome lengths and assembly information