AMR-Pathfinder

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

WF1: AbritAMR / AMRFinderPlus
WF2: Sciensano (not currently included)
WF3: SRST2
WF4: StarAMR

Installation

You will need to:
- run the RGI Database Builder as a Galaxy admin (if this hasn't been done already)
- Have the en_US.UTF-8 locale installed on the compute nodes executing cast/melt jobs.
- Install the requisite tools with e.g. shed-tools command from the ephemeris suite: shed-tools install -g https://galaxy.example.com -a API_KEY -t tools.yaml (tools.yaml is provided in this repository.)
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	Sanitize Filename	n/a
7	Shovill	toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy1
8	WF3: SRST2 :: AMR - SeqSero2/SISTR	n/a
9	Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4
10	benchAMRking: wf1	n/a
11	benchAMRking: wf3b	n/a
12	ABRicate	toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1
13	staramr	toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1
14	Add column	addValue
15	Add column	addValue
16	Add column	addValue
17	hamronize	toolshed.g2.bx.psu.edu/repos/iuc/hamronize_tool/hamronize_tool/1.0.3+galaxy1
18	hamronize	toolshed.g2.bx.psu.edu/repos/iuc/hamronize_tool/hamronize_tool/1.0.3+galaxy1
19	Select	Grep1
20	Collapse Collection	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
21	Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4
22	hamronize summarize:	toolshed.g2.bx.psu.edu/repos/iuc/hamronize_summarize/hamronize_summarize/1.1.4+galaxy0
23	hamronize: summarize	toolshed.g2.bx.psu.edu/repos/iuc/hamronize_summarize/hamronize_summarize/1.0.3+galaxy2
24	hamronize: summarize	toolshed.g2.bx.psu.edu/repos/iuc/hamronize_summarize/hamronize_summarize/1.0.3+galaxy2
25	Select	Grep1
26	Split file	toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.2
27	Cut	Cut1
28	Select	Grep1
29	Add column	addValue
30	Merge collections	__MERGE_COLLECTION__
31	Apply rules	__APPLY_RULES__
32	Concatenate multiple datasets	toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.3
33	Move WF# col to second position, keep score	Cut1
34	Move WF# col to second position 2, delete score	Cut1
35	Datamash	toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0
36	Add column	addValue
37	Concatenate datasets	cat1
38	Concatenate datasets	cat1
39	% Identity	toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2
40	Binary Comparison	toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2

Version History