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1 SoftSearch:
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2
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3 --SoftSearch is a tool that uses soft-masked reads and discordant read pairs to identify structural variants(SV) in
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4 Illumina paired-end next-generation sequencing data.
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5 --Using Soft Clipped reads in which one part of the read maps to the reference genome but the other part does not SoftSearch
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6 can identify and call SVs including deletions, insertions, translocations, inversions, and tandem duplications
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7 --SoftSearch requires two inputs: a BAM file of aligned reads and fasta file of the reference genome to which the reads
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8 were aligned.
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9
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10 Google Code Link:
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11
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12 https://code.google.com/p/softsearch/
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13
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14 ------------------------------------------------------------------------------------------------------------------
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15 Pre-Requirement:
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16
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17 -Perl
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18 -Bedtools
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19 -SamTools
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20 Must be accessible from the PATH environment variable
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21
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22 ------------------------------------------------------------------------------------------------------------------
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23 How To Select fasta file from Database (Additional Configuration):
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24
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25 --A fasta_indexes.loc file must be located in shed_tools/toolshed.g2.bx.psu.edu/repos/plus91-technologies/softsearch/
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26 8578d978014c/softsearch/tool-data/
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27
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28 --open the fasta_indexes.loc file and add an entry according to the example below
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30 <unique_build_id> <dbkey> <display_name> <file_base_path>
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31
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32 eg: hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
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33
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34 --open shed_tool_data_table_conf.xml file and add the following
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35
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36 <tables>
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37 <table name="fasta_indexes" comment_char="#">
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38 <columns>value, dbkey, name, path</columns>
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39 <file path="/path/to/fasta_indexes.loc" />
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40 </table>
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41 </tables>
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42
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43 ------------------------------------------------------------------------------------------------------------------
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44 Authors:
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45
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46 ResearchDx
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47 http://researchdx.com
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48
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49 Plus91 Technologies Private Limited
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50 http://www.plus91.in/
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