This directory contains the Nov. 2009 (SGSC Sscrofa9.2/susScr2) assembly
of the pig genome (susScr2, SGSC Sscrofa9.2
(NCBI project 10718, GCA_000003025.2)), as well as repeat
annotations and GenBank sequences.
This assembly was produced by the Swine Genome Sequencing Consortium
and Wellcome Trust Sange Institute.
For more information on the pig genome, see the project website:
http://piggenome.org/
http://www.sanger.ac.uk/resources/
Files included in this directory:
susScr2.2bit - contains the complete pig/susScr2 genome sequence
in the 2bit file format. 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/cvs.html
http://genome.ucsc.edu/admin/jk-install.html
chromAgp.tar.gz - Description of how the assembly was generated from
fragments, unpacking to one file per chromosome.
chromFa.tar.gz - The assembly sequence in one file per chromosome.
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.
chromFaMasked.tar.gz - The assembly sequence in one file per chromosome.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
chromOut.tar.gz - RepeatMasker .out files (one file per chromosome).
RepeatMasker was run with the -s (sensitive) setting.
June 4 2009 (open-3-2-8) version of RepeatMasker
RepeatMaskerLib.embl version: 20090604;
chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into UCSC's BED 5+
format (one file per chromosome).
est.fa.gz - Pig ESTs in GenBank. This sequence data is updated once a
week via automatic GenBank updates.
md5sum.txt - checksums of files in this directory
mrna.fa.gz - Pig mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
xenoMrna.fa.gz - GenBank mRNAs from species other than that of
the genome. This sequence data is updated once a week via automatic
GenBank updates.
susScr2.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
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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/susScr2/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/susScr2/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/susScr2/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/susScr2/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/susScr2/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
Name Last modified Size Description
Parent Directory -
chromAgp.tar.gz 2010-03-31 10:25 2.7M
chromFa.tar.gz 2010-03-31 10:36 701M
chromFaMasked.tar.gz 2010-03-31 10:43 423M
chromOut.tar.gz 2010-03-31 10:26 128M
chromTrf.tar.gz 2010-03-31 10:43 5.7M
est.fa.gz 2019-10-17 21:39 274M
est.fa.gz.md5 2019-10-17 21:39 44
genes/ 2020-02-05 13:47 -
md5sum.txt 2010-05-11 15:25 301
mrna.fa.gz 2019-10-17 21:21 21M
mrna.fa.gz.md5 2019-10-17 21:21 45
susScr2.2bit 2010-03-26 09:08 567M
susScr2.chrom.sizes 2010-03-25 12:50 299
susScr2.fa.gz 2020-01-23 02:26 701M
upstream1000.fa.gz 2019-10-17 21:40 1.7M
upstream1000.fa.gz.md5 2019-10-17 21:40 53
upstream2000.fa.gz 2019-10-17 21:40 3.3M
upstream2000.fa.gz.md5 2019-10-17 21:40 53
upstream5000.fa.gz 2019-10-17 21:40 8.0M
upstream5000.fa.gz.md5 2019-10-17 21:40 53
xenoMrna.fa.gz 2019-10-17 21:32 6.8G
xenoMrna.fa.gz.md5 2019-10-17 21:32 49
xenoRefMrna.fa.gz 2019-10-17 21:39 328M
xenoRefMrna.fa.gz.md5 2019-10-17 21:39 52