Workflow Type: Galaxy
Work-in-progress

This is an aggregation of the work done in Seq4AMR consisting of the following workflows:

Installation

  • You will need to:
  • Then you can import this workflow
    • Navigate to /workflows/import of your Galaxy server
    • Select "GA4GH servers"
    • Enter name:"AMR-Pathfinder"
  • And run it
    • You must provide a Sequencing collection (list:paired of fastq files)
    • And a Genomes collection (list of fasta files)
    • Both of these should use identical collection element identifiers

Outputs

This will produce two important tables: "Binary Comparison" and a "% Identity Scored Outputs".

Binary comparison

This file reports the discovery or absence of specific AMR genes across all tested AMR Analysis tools. You will mostly see 1s (presence) or 0s (absence) but you may occasionally see higher numbers when an AMR tool reports multiple hits for a specific gene.

% Identity Scored Outputs

This is similar to binary comparison, but using the % identity reported by each AMR tool. For cases where multiple hits were detected, we take the highest.

Known Issues

The names for identified AMR genes is highly inconsistent across AMR analysis tools. We urge the AMR community to rectify this by standardising gene names used in their tooling.

Steps

ID Name Description
5 Create text file toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0
6 Sanitise Filename n/a
7 Extract element identifiers toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
8 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4
9 benchAMRking: wf1 n/a
10 benchAMRking: wf3b n/a
11 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2
12 Add column addValue
13 Add column addValue
14 Relabel identifiers __RELABEL_FROM_FILE__
15 WF3: SRST2 :: AMR - SeqSero2/SISTR n/a
16 Shovill toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy1
17 Add column addValue
18 ABRicate toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1
19 staramr toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1
20 Select Grep1
21 hamronize toolshed.g2.bx.psu.edu/repos/iuc/hamronize_tool/hamronize_tool/1.0.3+galaxy1
22 hamronize toolshed.g2.bx.psu.edu/repos/iuc/hamronize_tool/hamronize_tool/1.0.3+galaxy1
23 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
24 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4
25 hamronize summarize: toolshed.g2.bx.psu.edu/repos/iuc/hamronize_summarize/hamronize_summarize/1.1.4+galaxy0
26 hamronize: summarize toolshed.g2.bx.psu.edu/repos/iuc/hamronize_summarize/hamronize_summarize/1.0.3+galaxy2
27 hamronize: summarize toolshed.g2.bx.psu.edu/repos/iuc/hamronize_summarize/hamronize_summarize/1.0.3+galaxy2
28 Select Grep1
29 Split file toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.2
30 Cut Cut1
31 Select Grep1
32 Add column addValue
33 Merge collections __MERGE_COLLECTION__
34 Apply rules __APPLY_RULES__
35 Concatenate multiple datasets toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.3
36 Move WF# col to second position, keep score Cut1
37 Move WF# col to second position 2, delete score Cut1
38 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0
39 Add column addValue
40 Concatenate datasets cat1
41 Concatenate datasets cat1
42 % Identity toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2
43 Binary Comparison toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2

Version History

Version 4.7 (latest) Created 14th Nov 2024 at 14:57 by Helena Rasche

Sanitise filenames for input collections


Open master 9d84881

Version 4.6 (earliest) Created 28th Oct 2024 at 13:43 by Helena Rasche

Initial working version of the AMR Pathfinder project workflow


Frozen Version-4.6 a29814d
help Creators and Submitter
License
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Views: 763   Downloads: 75   Runs: 8

Created: 28th Oct 2024 at 13:43

Last updated: 4th Nov 2024 at 15:04

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