This directory contains the Sierra Leone 2014 (G3683/KM034562.1/eboVir3)
assembly of the Ebola virus 2014 genome
(eboVir3, West Africa 01 June 2014 EBOV/G3683/KM034562.1).
For more information about this assembly, please note the NCBI resources:
http://www.ncbi.nlm.nih.gov/genome/4887
http://www.ncbi.nlm.nih.gov/genome/assembly/KM034561
http://www.ncbi.nlm.nih.gov/bioproject/257197
Files included in this directory:
eboVir3.2bit - contains the complete Ebola virus 2014/eboVir3 genome sequence
in the 2bit file format. There are no repeats, there is no repeat masking.
The utility program, twoBitToFa (available
from the kent src tree), can be used to extract .fa file(s) from
this file. A pre-compiled version of the command line tool can be
found at:
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
See also:
http://genome.ucsc.edu/admin/git.html
http://genome.ucsc.edu/admin/jk-install.html
KM034562v1.agp.gz - Description of how the assembly was generated from
fragments
KM034562v1.fa.gz - The single assembly sequence. There are no repeats,
there is no repeat masking
160sequences.tar.gz - fasta files for 158 sequences of Ebola,
and two sequences for Marburg virus. The file names are
the genbank accession identifiers. Extract sequences:
tar xvzf 160sequences.tar.gz
md5sum.txt - checksums of files in this directory
eboVir3.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
eboVir3.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
- to construct the GC Percent track
eboVir3.gc5Base.wig.gz - wiggle database table for the GC Percent track
- this is an older standard alternative to the current
- bigWig format of the track, sometimes usefull for analysis
eboVir3.gc5Base.wib - binary data to correspond with the gc5Base.wig file
see also: http://genome.ucsc.edu/goldenPath/help/wiggle.html
and http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database
for a discussion of how to use the wig.gz and .wib files for
interaction with the GC percent data values
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If you plan to download a large file or multiple files from this
directory, we recommend that you use ftp rather than downloading the
files via our website. To do so, ftp to hgdownload.cse.ucsc.edu
[username: anonymous, password: your email address], then cd to the
directory goldenPath/eboVir3/bigZips. To download multiple files, use
the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Alternate methods to ftp access.
Using an rsync command to download the entire directory:
rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/bigZips/chromFa.tar.gz'
-O chromFa.tar.gz
To unpack the *.tar.gz files:
tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
gunzip <file>.fa.gz
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GenBank Data Usage
The GenBank database is designed to provide and encourage access within
the scientific community to the most up to date and comprehensive DNA
sequence information. Therefore, NCBI places no restrictions on the use
or distribution of the GenBank data. However, some submitters may claim
patent, copyright, or other intellectual property rights in all or a
portion of the data they have submitted. NCBI is not in a position to
assess the validity of such claims, and therefore cannot provide comment
or unrestricted permission concerning the use, copying, or distribution
of the information contained in GenBank.
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Name Last modified Size Description
Parent Directory -
160sequences.tar.gz 2014-09-30 10:43 717K
KM034562v1.agp.gz 2014-09-18 09:31 63
KM034562v1.fa.gz 2014-09-30 09:44 6.2K
eboVir3.2bit 2014-09-18 09:31 4.7K
eboVir3.chrom.sizes 2014-09-18 09:31 17
eboVir3.fa.gz 2020-01-23 02:21 6.2K
eboVir3.gc5Base.wib 2019-01-17 14:46 3.7K
eboVir3.gc5Base.wig.gz 2019-01-17 14:46 184
eboVir3.gc5Base.wigVarStep.gz 2014-09-18 09:36 9.7K
md5sum.txt 2019-01-17 15:53 424