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28
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1 SoftSearch:
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2
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3 --SoftSearch is a tools that uses soft-masked reads and discordant read pairs to identify structural variation(SV) in
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4 illumina next-generation sequencing data.
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5 --It is a Integration of Multiple Sequence Features to Identify Breakpoints of Structural Variations.
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6 --Breakpoint is a place or time at which an interruption or change is made.
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7 --SoftSearch requires only two inputs: a BAM file of aligned reads and fasta file of the genome to which the reads were aligned.
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8
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9 Google Code Link:
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10
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11 https://code.google.com/p/softsearch/
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12
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13 ------------------------------------------------------------------------------------------------------------------
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14 Pre-Requirement:
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15
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16 -Perl
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17 -Bedtools
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18 -SamTools
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19 Must have an entry in environment variable
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20
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21 ------------------------------------------------------------------------------------------------------------------
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22 How To Selecte fasta file from Database (Additional Configuration):
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23
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24 --Select fasta_indexes.loc file for that go to shed_tools/toolshed.g2.bx.psu.edu/repos/plus91-technologies/softsearch/
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25 8578d978014c/softsearch/tool-data/
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26
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27 --open the fasta_indexes.loc file and make changes like
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28
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29 <unique_build_id> <dbkey> <display_name> <file_base_path>
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30
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31 eg: hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
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32
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33 --open shed_tool_data_table_conf.xml file and add following.
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34
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35 <tables>
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36 <table name="fasta_indexes" comment_char="#">
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37 <columns>value, dbkey, name, path</columns>
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38 <file path="/path/to/fasta_indexes.loc" />
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39 </table>
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40 </tables>
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41
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42 ------------------------------------------------------------------------------------------------------------------
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43 Authors:
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44
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45 ResearchDx
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46 http://researchdx.com
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47
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48 Plus91 Technologies Private Limited
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49 http://www.plus91.in/
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