Assembly-decontamination-VGP9
1.0

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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

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1359?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

1.0 (earliest) Created 9th Sep 2024 at 14:23 by Helena Rasche

Added/updated 4 files


Open master d72104b
help Creators and Submitter
Creators
Not specified
Submitter
Tools
BLAST
kraken2
gfastats
License
BSD 3-Clause "New" or "Revised" License
Activity

Views: 203   Downloads: 61

Created: 9th Sep 2024 at 14:23

Last updated: 9th Sep 2024 at 14:23

help Attributions

None

Total size: 122 KB
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