diff --git a/ChangeLog b/ChangeLog index 945feb6..3ec4dc4 100755 --- a/ChangeLog +++ b/ChangeLog @@ -3,6 +3,7 @@ ChangeLog of HGTector == Version 0.2.2 (8/23/2017) == New features: +- Provided a pre-built standard database. - Added an installation script "installer.sh". - Adopted new NCBI standard, i.e., using accession instead of GI as sequence identifier. - Modified the mechanism of databaser.py. Now it downloads both DNA and protein sequences. diff --git a/HGTector.pl b/HGTector.pl index 8f4eae7..0d0bca7 100644 --- a/HGTector.pl +++ b/HGTector.pl @@ -74,12 +74,16 @@ } print "\n"; - print "Now I will assist you to generate a reference database.\n"; - print "Unless you plan to use HGTector in remote mode, a local reference database is recommended for consistant and controllable analyses.\n"; + print "Now I will assist you to prepare a reference database.\n"; + print "Unless you plan to always use HGTector in remote mode, a local reference database is recommended for consistant and controllable analyses.\n"; + print "The database will have three components: a protein sequence database, a taxonomy database, and a protein-to-taxonomy dictionary.\n"; + print "Using proper databases is important for optimal results. Please consider reading about the details of choice of databases in the GUI.\n"; + print "\n"; + + print "A pre-built database is available (see README.md for download link). Alternatively, I will build an up-to-date one for you now.\n"; print "Proceed (YES/no)? "; $s = ; chomp $s; if (not $s or $s =~ /^yes$/i or $s =~ /^y$/i) { - print "HGTector requires three databases: a protein sequence database, a taxonomy database, and a protein-to-taxonomy dictionary. Using proper databases is important for optimal results. Please read about the details of choice of databases in the GUI.\n"; print "\nPlease specify a location to store the databases (default: db/ in the program directory): "; $s = ; chomp $s; $s =~ s/\/$//; $db = $s if $s; @@ -110,7 +114,7 @@ } my $i = system "python $scripts/databaser.py -format=$format -range=$range -represent=$represent -subsample=$subsample -out=$out"; chdir $cwd; - print "\nThere appear to be some problems in database building.\n" unless -s "$db/$out.faa"; + print "\nThere appears to be some problems in database building.\n" unless -s "$db/$out.faa"; print "\nNow that databases are created. Your may link HGTector to them in future analyses, by setting the following parameters in config.txt:\n"; if ($format eq "blast") { print "protdb=$db/blast/$out\n"; diff --git a/README.md b/README.md index 09040b1..6f42785 100644 --- a/README.md +++ b/README.md @@ -1,23 +1,17 @@ HGTector -========== - -**Note: Instead of downloading the release, please git clone the master branch, which contains an important update in match with the new NCBI FTP site structure.** - -**Alternatively, please download a pre-constructed database from [here](https://u21438014.dl.dropboxusercontent.com/u/21438014/HGTector/stdb_20170128.tar.xz).** +======== A computational pipeline for genome-wide detection of putative horizontal gene transfer (HGT) events based on sequence homology search hit distribution statistics -Latest release: [0.2.1](https://github.com/DittmarLab/HGTector/archive/0.2.2.zip) - -Last update: 2017-1-28 - Authors: Qiyun Zhu (), Katharina Dittmar () Affiliation: Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, USA License: [BSD 2-clause](http://opensource.org/licenses/BSD-2-Clause). -An article detailing the method and its performance on simulated and real genomic datasets can be found [here](http://www.biomedcentral.com/1471-2164/15/717): +Download the latest release: [0.2.2](https://github.com/DittmarLab/HGTector/archive/0.2.2.zip), updated on 2017-8-23; and a standard [database](https://u21438014.dl.dropboxusercontent.com/u/21438014/HGTector/stdb_20170630.tar), updated on 2017-6-30. + +An article detailing the method and its performance on simulated and real genomic datasets can be found [here](https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-717): Zhu Q, Kosoy M, Dittmar K. HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers. *BMC Genomics*. 2014. 15:717. @@ -25,4 +19,4 @@ Please visit our lab's [website](http://katharina-dittmar.squarespace.com/) for Usage: Simply execute **perl HGTector.pl**, or, open **GUI.html** in a web browser to see a step-by-step wizard. -Download [HGTector 0.2.1](https://github.com/DittmarLab/HGTector/archive/0.2.1.zip). +Download [HGTector 0.2.2](https://github.com/DittmarLab/HGTector/archive/0.2.2.zip).