bacterial-genome-assembly/main

View on GitHub Download RO-Crate Run on Galaxy
Workflow Type: Galaxy

Assembly of bacterial paired-end short read data with generation of quality metrics and reports

SEEK ID: https://workflowhub.eu/workflows/1150?version=2

Inputs

ID Name Description Type
Input adapter trimmed sequence reads (forward) #main/Input adapter trimmed sequence reads (forward) Should be the adapter trimmed forward strand of the paired end reads.
  • File
Input adapter trimmed sequence reads (reverse) #main/Input adapter trimmed sequence reads (reverse) Should be the adapter trimmed reverse strand of the paired end reads.
  • File

Steps

ID Name Description
2 shovill_genome_assembly genome assembly with shovill tool toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy2
3 quast_quality quast_quality toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1
4 refseqmasher_genome refseqmasher_genome, search close reference genome in refseq database toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_matches/0.1.2
5 bandage_contig_graph_stats bandage_contig_graph_stats toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/2022.09+galaxy2
6 bandage_contig_graph_plot bandage_contig_graph_plot toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
7 ToolDistillator ToolDistillator extracts results from tools and creates a JSON file for each tool toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0
8 ToolDistillator summarize ToolDistillator summarize groups all JSON file into a unique JSON file toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0

Outputs

ID Name Description Type
bandage_contig_graph_plot #main/bandage_contig_graph_plot n/a
  • File
bandage_contig_graph_stats #main/bandage_contig_graph_stats n/a
  • File
quast_log #main/quast_log n/a
  • File
quast_report_html #main/quast_report_html n/a
  • File
quast_report_pdf #main/quast_report_pdf n/a
  • File
quast_report_tabular #main/quast_report_tabular n/a
  • File
refseqmasher_report_tabular #main/refseqmasher_report_tabular n/a
  • File
shovill_alignment_bam #main/shovill_alignment_bam n/a
  • File
shovill_contigs_fasta #main/shovill_contigs_fasta n/a
  • File
shovill_contigs_graph #main/shovill_contigs_graph n/a
  • File
shovill_logfile #main/shovill_logfile n/a
  • File
tooldistillator_results #main/tooldistillator_results n/a
  • File
tooldistillator_summarize #main/tooldistillator_summarize n/a
  • File

Version History

v1.1.2 (latest) Created 20th Sep 2024 at 03:02 by WorkflowHub Bot

Updated to v1.1.2


Frozen v1.1.2 22b88f9

v1.1.1 (earliest) Created 7th Sep 2024 at 03:04 by WorkflowHub Bot

Updated to v1.1.1


Frozen v1.1.1 6f19bd0
help Creators and Submitter
Creators
Additional credit

abromics-consortium

Submitter
License
GNU General Public License v3.0 or later
Activity

Views: 113   Downloads: 19   Runs: 1

Created: 7th Sep 2024 at 03:04

help Tags

This item has not yet been tagged.

help Attributions

None

Total size: 40.2 KB
Powered by
 (v.1.16.0-main)
About WorkflowHub | Acknowledgements | Credits | Terms & Conditions | Privacy Policy | Cite us | Contact us
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH