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author iuc
date Mon, 28 Apr 2025 07:17:59 +0000
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1 <macros>
1
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2 <token name="@TOOL_VERSION@">1.7.1</token>
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3 <token name="@VERSION_SUFFIX@">0</token>
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4 <xml name="citations">
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5 <citations>
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6 <citation type="doi">10.1186/S13059-019-1911-0</citation>
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7 </citations>
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8 </xml>
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9 <xml name="requirements">
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10 <requirements>
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11 <requirement type="package" version="@TOOL_VERSION@">syri</requirement>
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12 </requirements>
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13 </xml>
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14 <xml name="help">
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15 <help><![CDATA[
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16 SyRI (Synteny and Rearrangement Identifier)
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17 ===========================================
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18 SyRI identifies structural rearrangements and local variations between two chromosome-level genome assemblies. It analyzes alignments from whole-genome alignment tools (like minimap2) and produces annotations of syntenic regions, inversions, translocations, duplications, SNPs, and indels.
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20 More Info
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21 ---------
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22 For more information please check the following links
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24 - Tool homepage: https://github.com/schneebergerlab/syri
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25 - Tutorial & documentation: https://schneebergerlab.github.io/syri/
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27 Inputs
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28 ------
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30 - **Alignment file** (`BAM`, `SAM`, or `PAF`) from a whole-genome aligner like minimap2
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31 - **Reference genome** (FASTA)
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32 - **Query genome** (FASTA)
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34 Outputs
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35 -------
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37 - **Main output**: a TSV format file of annotated regions (synteny + rearrangements)
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38 - **Summary**: Statistics on structural events
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39 - **VCF**: Local variations (SNPs, indels)
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40 - **Map IDs**: Chromosome name mapping between reference and query (only populated if chromosome names differ)
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41
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42 Notes:
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43 ------
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45 - The **Map IDs file** lists corresponding chromosomes between the reference and query genomes. This file is **only generated** by SyRI when the chromosome names **differ** between the two genomes. If the chromosome names are identical, the file will be **empty** — this is expected and not an error.
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46 - When using **minimap2** to generate alignments for SyRI, the **minimum required Galaxy wrapper version is `2.28+galaxy1`**. This version correctly adds the `--eqx` flag, which is **required** by SyRI to interpret alignment CIGAR strings properly.
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48 Common Options
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49 --------------
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50 • **--seed**
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51 Seed for generating random numbers.
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52 *Galaxy field:* “Seed for generating random numbers (default 1)”
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54 • **-f**
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55 Use the full list of alignments without filtering (default off).
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56 *Galaxy field:* “Disable filtering of low-quality and small alignments”
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57
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58 • **--samplename**
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59 Sample name to be used in the output VCF file (default sample).
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60 *Galaxy field:* “Sample name for the output VCF file”
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61
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62 • **--no-chrmatch**
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63 Prevents automatic matching of chromosome IDs between the reference and query genomes.
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64 *Galaxy field:* “Prevent automatic matching of chromosome IDs between genomes”
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66 Example Usage:
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67 --------------
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69 .. code-block:: bash
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71 syri -c aln.bam -r ref.fasta -q qry.fasta -F B
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72 ]]></help>
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73 </xml>
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74 </macros>