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 ------------------------------------------------------------------ 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 ... - 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 .tar.gz To uncompress the fa.gz files: gunzip .fa.gz ----------------------------------------------------------------------------- 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. -----------------------------------------------------------------------------