Quality and contamination control in bacterial isolate using Illumina MiSeq Data

Bérénice Batut, Clea Siguret

Last updated Jul 15, 2024

Launch in Tutorial Mode question
License: GPL-3.0-or-later
Tests: ✅ Results: Not yet automated

flowchart TD
  0["ℹ️ Input Dataset\nDRR187559_1"];
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  1["ℹ️ Input Dataset\nDRR187559_2"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["FastQC forward"];
  0 -->|output| 2;
  d3aed14e-51b8-40b0-9d6d-548fff2ab63a["Output\nFastQC text_file (forward)"];
  2 --> d3aed14e-51b8-40b0-9d6d-548fff2ab63a;
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  6c927338-7e02-4599-a01d-014a35a529e8["Output\nFastQC html_file (forward)"];
  2 --> 6c927338-7e02-4599-a01d-014a35a529e8;
  style 6c927338-7e02-4599-a01d-014a35a529e8 stroke:#2c3143,stroke-width:4px;
  3["FastQC reverse"];
  1 -->|output| 3;
  30d76c09-809d-4415-a1e6-f244cfc34065["Output\nFastQC html_file (reverse)"];
  3 --> 30d76c09-809d-4415-a1e6-f244cfc34065;
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  bbafb072-8b12-4908-ae0f-10cc7f9086d3["Output\nFastQC text_file (reverse)"];
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  4["fastp"];
  0 -->|output| 4;
  1 -->|output| 4;
  1a089ca0-445a-4322-b74f-60c7aefc7cd8["Output\nfastp report_html"];
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  b634addf-dcb8-43e6-8016-341de7eb5b87["Output\nDRR187559_filtered_"];
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  0a57afa4-e75e-470d-ad7b-13e567ce54a3["Output\nDRR187559_filtered_1"];
  4 --> 0a57afa4-e75e-470d-ad7b-13e567ce54a3;
  style 0a57afa4-e75e-470d-ad7b-13e567ce54a3 stroke:#2c3143,stroke-width:4px;
  bb98c4d1-bd1d-47bd-ac56-4ac0e1e49d50["Output\nfastp_json"];
  4 --> bb98c4d1-bd1d-47bd-ac56-4ac0e1e49d50;
  style bb98c4d1-bd1d-47bd-ac56-4ac0e1e49d50 stroke:#2c3143,stroke-width:4px;
  5["Kraken2"];
  4 -->|out1| 5;
  4 -->|out2| 5;
  54b85a53-72ee-4b73-b186-7fd55e8aab9b["Output\nkraken_report_tabular"];
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  a408a644-58cd-4f5e-af25-15b5ea63aa76["Output\nkraken_report_reads"];
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  6["Bracken"];
  5 -->|report_output| 6;
  8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8["Output\nbracken_kraken_report"];
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  ae6c6464-f5f5-4e5b-b616-d38166fc0133["Output\nbracken_report_tsv"];
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  style ae6c6464-f5f5-4e5b-b616-d38166fc0133 stroke:#2c3143,stroke-width:4px;
  7["Recentrifuge"];
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