Assembly-decontamination-VGP9/main
Version 1

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SEEK ID: https://workflowhub.eu/workflows/860?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 lower to uppercase toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1
3 soft-masking toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy1
4 hard-masking toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1
5 ID non-target contaminants toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1
6 blast mitochondria DB toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy1
7 contaminant scaffolds toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
8 parsing blast output toolshed.g2.bx.psu.edu/repos/iuc/parse_mito_blast/parse_mito_blast/1.0.2+galaxy0
9 remove > + lowercase toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1
10 to lowercase toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1
11 isolate scaffolds names toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4
12 concatenate scaffold lists toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1
13 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
full contaminant + mito scaffold list full contaminant + mito scaffold list n/a
  • File
final decontaminated assembly final decontaminated assembly n/a
  • File

Version History

v0.1.4 (earliest) Created 1st May 2024 at 03:04 by WorkflowHub Bot

Updated to v0.1.4


Frozen v0.1.4 e46571e
help Creators and Submitter
Creators
Not specified
Additional credit

Nadolina Brajuka

Submitter
Tools
BLAST
kraken2
gfastats
License
BSD 3-Clause "New" or "Revised" License (BSD-3-Clause)
Activity

Views: 123

Created: 1st May 2024 at 03:04

help Attributions

None

Total size: 32.1 KB
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