Assembly-decontamination-VGP9
1.0

Workflow Type: Galaxy

Associated Tutorial

This workflows is part of the tutorial Decontamination of a genome assembly, available in the GTN

Features

Thanks to...

Workflow Author(s): Nadolina Brajuka

Tutorial Author(s): Delphine Lariviere

Tutorial Contributor(s): Saskia Hiltemann, Deepti Varshney, Delphine Lariviere, Björn Grüning, Bérénice Batut

gtn star logo followed by the word workflows

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

1.0 (earliest) Created 2nd Jun 2025 at 11:00 by GTN Bot

Added/updated 4 files


Open master 77b8111
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Views: 33   Downloads: 2   Runs: 0

Created: 2nd Jun 2025 at 11:00

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