This directory contains the July 2005 (Broad/echTel1) assembly of the tenrec genome (echTel1, Broad July 2005), as well as repeat annotations and GenBank sequences. For more information about this assembly, please note the NCBI resources: http://www.ncbi.nlm.nih.gov/genome/234 http://www.ncbi.nlm.nih.gov/genome/assembly/229058 http://www.ncbi.nlm.nih.gov/bioproject/12590 Files included in this directory: echTel1.2bit - contains the complete tenrec/echTel1 genome sequence in the 2bit file format. Repeats from RepeatMasker and Tandem Repeats Finder (with period of 12 or less) are shown in lower case; non-repeating sequence is shown in upper case. 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 echTel1.agp.gz - Description of how the assembly was generated from fragments. echTel1.fa.gz - "Soft-masked" assembly sequence in one file. Repeats from RepeatMasker and Tandem Repeats Finder (with period of 12 or less) are shown in lower case; non-repeating sequence is shown in upper case. echTel1.fa.masked.gz - "Hard-masked" assembly sequence in one file. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. echTel1.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the -s (sensitive) setting. April 26 2011 (open-3-3-0) version of RepeatMasker, RepeatMaskerLib.embl version: CC RELEASE 20110920 echTel1.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, and translated into UCSC's BED format. echTel1.qual.fa.gz - quality scores from the assembly process md5sum.txt - checksums of files in this directory echTel1.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. echTel1.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used - to construct the GC Percent track echTel1.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 echTel1.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 echTel1.chromAlias.txt - sequence name alias file, one line for each sequence name. First column is sequence name followed by tab separated alias names. ------------------------------------------------------------------ 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/echTel1/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/echTel1/bigZips/ . For a single file, e.g. chromFa.tar.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/echTel1/bigZips/chromFa.tar.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/echTel1/bigZips/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/echTel1/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 The Tenrec sequence is made freely available before scientific publication with the following understanding: 1. The data may be freely downloaded, used in analyses, and repackaged in databases. 2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data (The Broad Institute) is properly acknowledged. 3. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). 4. Any redistribution of the data should carry this notice. 1. The data may be freely downloaded, used in analyses, and repackaged in databases.
Name Last modified Size Description
Parent Directory - echTel1.2bit 2012-05-24 14:04 947M echTel1.agp.gz 2012-05-24 14:19 16M echTel1.chrom.sizes 2005-08-04 18:55 6.4M echTel1.chromAlias.bb 2022-09-08 22:08 47M echTel1.chromAlias.txt 2022-09-08 22:08 8.6M echTel1.fa.gz 2012-05-24 14:30 712M echTel1.fa.masked.gz 2012-05-24 14:41 522M echTel1.fa.out.gz 2012-05-24 14:20 87M echTel1.gc5Base.wib 2019-01-17 14:47 444M echTel1.gc5Base.wig.gz 2019-01-17 14:47 17M echTel1.gc5Base.wigVarStep.gz 2012-05-24 15:22 946M echTel1.qual.fa.gz 2008-11-24 14:05 942M echTel1.trf.bed.gz 2012-05-24 14:20 2.4M genes/ 2020-02-05 13:47 - md5sum.txt 2022-09-08 22:07 645 xenoRefMrna.fa.gz 2020-02-28 00:38 337M xenoRefMrna.fa.gz.md5 2020-02-28 00:38 52