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 -
genes/ 2020-02-05 13:47 -
xenoRefMrna.fa.gz.md5 2019-10-17 02:20 52
md5sum.txt 2019-01-17 15:53 532
trf.bed.gz 2005-08-04 18:08 2.4M
echTel1.trf.bed.gz 2012-05-24 14:20 2.4M
echTel1.chrom.sizes 2005-08-04 18:55 6.4M
echTel1.chromAlias.txt 2022-09-08 14:11 8.6M
echTel1.agp.gz 2012-05-24 14:19 16M
assembly.agp.gz 2005-08-02 08:40 16M
echTel1.gc5Base.wig.gz 2019-01-17 14:47 17M
echTel1.chromAlias.bb 2022-09-08 14:11 47M
rmsk.out.gz 2005-08-04 11:57 61M
echTel1.fa.out.gz 2012-05-24 14:20 87M
xenoRefMrna.fa.gz 2019-10-17 02:20 331M
echTel1.gc5Base.wib 2019-01-17 14:47 444M
echTel1.fa.masked.gz 2012-05-24 14:41 522M
scaffold.fa.gz 2005-08-03 11:48 666M
scaffoldSoftMask.fa.gz 2005-08-04 18:28 701M
echTel1.fa.gz 2012-05-24 14:30 712M
echTel1.qual.fa.gz 2008-11-24 14:05 942M
echTel1.gc5Base.wigVarStep.gz 2012-05-24 15:22 946M
echTel1.2bit 2012-05-24 14:04 947M