Assembly-decontamination-VGP9/main
v0.3

View on GitHub Download RO-Crate Run on Galaxy
Workflow Type: Galaxy
No description specified

SEEK ID: https://workflowhub.eu/workflows/1126?version=1

Inputs

ID Name Description Type
Database for Kraken2 Database for Kraken2 Select the database to query to identify non-target contaminants.
  • string
Scaffolded assembly (fasta) Scaffolded assembly (fasta) n/a
  • File

Steps

ID Name Description
2 soft-masking toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy2
3 hard-masking toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1
4 ID non-target contaminants toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1
5 blast mitochondria DB toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy2
6 Cut Cut1
7 parsing blast output toolshed.g2.bx.psu.edu/repos/iuc/parse_mito_blast/parse_mito_blast/1.0.2+galaxy0
8 Filter Filter1
9 Cut Cut1
10 concatenate scaffold lists toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1
11 removing scaffolds toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0

Outputs

ID Name Description Type
Kraken2 classification scores Kraken2 classification scores n/a
  • File
mito_scaff_names mito_scaff_names n/a
  • File
contaminants_table contaminants_table n/a
  • File
full contaminant + mito scaffold list full contaminant + mito scaffold list n/a
  • File
final decontaminated assembly final decontaminated assembly n/a
  • File

Version History

v0.3 (earliest) Created 7th Sep 2024 at 03:02 by WorkflowHub Bot

Updated to v0.3


Frozen v0.3 46290b3
help Creators and Submitter
Creators
Not specified
Additional credit

Nadolina Brajuka

Submitter
License
BSD 3-Clause "New" or "Revised" License
Activity

Views: 162   Downloads: 26   Runs: 0

Created: 7th Sep 2024 at 03:02

help Tags

This item has not yet been tagged.

help Attributions

None

Total size: 30.7 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