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3
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1 iAssembler tools for Galaxy
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2
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3 iAssembler is a standalone package to assemble ESTs generated using Sanger and/or Roche-454 pyrosequencing technologies into contigs.
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4 The pipeline gives much higher accuracy in EST assembly than other existing assemblers by employing an iterative assembly strategy and automated
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5 error corrections of mis-assemblies.
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6
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7 iAssembler first performs iterative assemblies using MIRA and CAP3 (default: four cycles of MIRA assemblies followed by one CAP3 assembly) to correct
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8 assembly errors (mostly sequences derived from the same transcript fail to be assembled together) which occur frequently in just one round of assembly.
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9
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10 The program then performs post-assembly quality checking by
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11 1) aligning each EST sequence to its corresponding unigene sequence to identify mis-assemblies; and
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12 2) performing all-verus-all pair-wise sequence alignments of unigenes to identify sequences derived from same transcripts that fail to be assembled together.
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13
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14 The identified mis-assemblies are then corrected by the program automatically.
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15
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16 http://bioinfo.bti.cornell.edu/tool/iAssembler/
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17
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18 Citation:
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19 Zheng Y, Zhao L, Gao J, Fei Z. (2011) iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences. BMC Bioinformatics 12:453
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20
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21 Galaxy XML and Perl wrapper script written by: Roger Ngo, Sam Min and Todd H. Oakley, UCSB
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22
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23 Included files in this package:
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24
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25 * iAssembler.xml - Galaxy XML tool for iAssembler 1.3
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26 * iAssembler_wrapper.pl - Wrapper script for Galaxy XML tool
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27 * increment.txt - File required by iAssembler_wrapper.pl
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28 * iAssembler_README - Documentation file
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29
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30 Note: iAssembler.pl MUST BE modified in lines 254-258 due to a bug preventing the program from working in the Galaxy platform.
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31
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32 Pre-Installation:
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33
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34 iAssembler 1.3 must be installed on the Galaxy user account. In order for the Galaxy tool wrapper to work, the iAssembler.pl
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35 script must be modified on lines 254-258.
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36
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37 FROM:
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38
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39 my $version_file = $working_dir."/mira_version";
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40 system("$program_bin_dir/mira | head > $version_file");
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41
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42 TO:
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43
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44 my $version_file = $working_dir."/mira_version";
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45 system("$program_bin_dir/mira > $working_dir/out");
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46 system("head $working_dir/out > $version_file");
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47
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48
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49 Installation Instructions:
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50
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51 1. Copy the iAssembler folder to a directory in your Galaxy user account.
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52
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53 2. Copy iAssembler.xml, iAssembler_wrapper.pl and increment.txt to a folder in /galaxy-dist/tools/
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54
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55 Note: increment.txt and iAssembler_wrapper.pl MUST be in the same directory.
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56
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57 3. In iAssembler_wrapper.pl, modify the $iAssemblerBinPath to point to the iAssembler 1.3 directory in your
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58 Galaxy user account and $iAssemblerToolPath to the path of the wrapper.
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59
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60 By default they have already been assigned as:
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61
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62 my $iAssemblerBinPath = '/labdata/nfs/galaxy/pkgs/iAssembler';
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63 my $iAssemblerToolPath = '/labdata/nfs/galaxy/galaxy-dist/tools/iAssembler';
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64
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65 4. Add the Galaxy tool information to tool_conf.xml in /galaxy-dist/
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66
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67 5. Restart Galaxy using
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68
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69 ./run.sh --stop-daemon
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70
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71 and then
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72
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73 ./run.sh --reload --daemon |
