bacterial-quality-and-contamination-control-post-assembly/main
v1.0

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Workflow Type: Galaxy

This workflow performs quality and contamination control analysis on assembled contigs to assess bacterial genome quality and taxonomic assignment

SEEK ID: https://workflowhub.eu/workflows/1882?version=1

Inputs

ID Name Description Type
Fasta boolean #main/Fasta boolean True if fasta metaWF False if fastq metaWF
  • boolean
Fastq boolean #main/Fastq boolean True if fastq metaWF False if fasta metaWF
  • boolean
Input sequence contigs FASTA #main/Input sequence contigs FASTA Fasta as contigs from raw reads assembly.
  • File
Input sequence reads (forward) #main/Input sequence reads (forward) Should be the forward strand of the paired end reads.
  • File
Input sequence reads (reverse) #main/Input sequence reads (reverse) Should be the reverse strand of the paired end reads.
  • File
Select a NCBI taxonomy database #main/Select a NCBI taxonomy database Select the ncbi taxonomy database for Recentrifuge.
  • string
Select a taxonomy database #main/Select a taxonomy database Select the database to use for assigning taxonomies for Kraken2 and Bracken.
  • string

Steps

ID Name Description
7 pick_R1_reads_with_fastq When the fastq metaWF is used, the R1 trimmed file is selected toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
8 pick_R2_reads_with_fastq When the fastq metaWF is used, the R2 trimmed file is selected toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
9 quast_quality_fasta quast_quality_fasta toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0
10 checkm2_quality Checkm2 to predict the completeness and contamination in an assembly toolshed.g2.bx.psu.edu/repos/iuc/checkm2/checkm2/1.0.2+galaxy1
11 kraken_taxonomy_assignation kraken_taxonomy_assignation toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1
12 quast_quality_fastq quast_quality_fastq toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0
13 collapse_checkm2_protein_collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
14 collapse_checkm2_diamond_collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
15 bracken_abundance_estimation bracken_abundance_estimation toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.1+galaxy0
16 recentrifuge_taxonomy_visualization recentrifuge_taxonomy_visualization toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.16.1+galaxy0
17 pick_generate_tabular_quast_report toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
18 pick_generate_html_quast_report toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
19 ToolDistillator ToolDistillator extracts results from tools and creates a JSON file for each tool toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.0+galaxy1
20 ToolDistillator summarize ToolDistillator summarize groups all JSON file into a unique JSON file toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.0+galaxy1

Outputs

ID Name Description Type
Bracken Kraken tabular report #main/Bracken Kraken tabular report n/a
  • File
Bracken tabular report #main/Bracken tabular report n/a
  • File
Checkm2 diamond files #main/Checkm2 diamond files n/a
  • File
Checkm2 protein files #main/Checkm2 protein files n/a
  • File
Checkm2 tabular report #main/Checkm2 tabular report n/a
  • File
Kraken2 sequence assignation #main/Kraken2 sequence assignation n/a
  • File
Kraken2 tabular report #main/Kraken2 tabular report n/a
  • File
QUAST tabular report for FASTQ files #main/QUAST tabular report for FASTQ files n/a
  • File
Quast HTMl report for FASTA files #main/Quast HTMl report for FASTA files n/a
  • File
Quast HTMl report for FASTQ files #main/Quast HTMl report for FASTQ files n/a
  • File
Quast tabular report for FASTA files #main/Quast tabular report for FASTA files n/a
  • File
Recentrifuge HTML report #main/Recentrifuge HTML report n/a
  • File
Recentrifuge data tabular report #main/Recentrifuge data tabular report n/a
  • File
Recentrifuge tabular statistics report #main/Recentrifuge tabular statistics report n/a
  • File
Tooldistillator results control #main/Tooldistillator results control n/a
  • File
Tooldistillator summarize control #main/Tooldistillator summarize control n/a
  • File

Version History

v1.0 (earliest) Created 22nd Aug 2025 at 03:02 by WorkflowHub Bot

Updated to v1.0


Frozen v1.0 0174a64
help Creators and Submitter
Creators
Additional credit

abromics-consortium

Submitter
Tools
QUAST
CheckM
kraken2
Bracken
Recentrifuge
ToolDistillator
License
GNU General Public License v3.0 or later
Activity

Views: 28   Downloads: 6   Runs: 0

Created: 22nd Aug 2025 at 03:02

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