assembly_with_preprocessing

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Workflow Type: Galaxy

Assembly with preprocessing

Associated Tutorial

This workflows is part of the tutorial assembly_with_preprocessing, available in the GTN

Thanks to...

Tutorial Author(s): Wolfgang Maier

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1132?version=2

Inputs

ID Name Description Type
Collection of long-reads data Collection of long-reads data n/a
  • File[]
Collection of paired short-reads data Collection of paired short-reads data n/a
  • File[]

Steps

ID Name Description
10 Samtools fastx toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1
11 Samtools fastx toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1
12 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2
13 Zip Collection __ZIP_COLLECTION__
14 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2
15 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2
16 seqtk_sample toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2
17 seqtk_sample toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2
18 Create assemblies with Unicycler toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0
19 Bandage Info toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1
2 fastp: Trimmed Illumina Reads toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1
20 Filter sequences by length toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2
21 Bandage Image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2
3 NanoPlot toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1
4 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1
5 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7
6 Bowtie2 toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0
7 Samtools view toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1
8 Samtools stats toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
9 Samtools view toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1

Outputs

ID Name Description Type
_anonymous_output_3 _anonymous_output_3 n/a
  • File
_anonymous_output_4 _anonymous_output_4 n/a
  • File
_anonymous_output_5 _anonymous_output_5 n/a
  • File
_anonymous_output_6 _anonymous_output_6 n/a
  • File
_anonymous_output_7 _anonymous_output_7 n/a
  • File
_anonymous_output_8 _anonymous_output_8 n/a
  • File
_anonymous_output_9 _anonymous_output_9 n/a
  • File
_anonymous_output_10 _anonymous_output_10 n/a
  • File
_anonymous_output_11 _anonymous_output_11 n/a
  • File
_anonymous_output_12 _anonymous_output_12 n/a
  • File
_anonymous_output_13 _anonymous_output_13 n/a
  • File
_anonymous_output_14 _anonymous_output_14 n/a
  • File
_anonymous_output_15 _anonymous_output_15 n/a
  • File
_anonymous_output_16 _anonymous_output_16 n/a
  • File
_anonymous_output_17 _anonymous_output_17 n/a
  • File
_anonymous_output_18 _anonymous_output_18 n/a
  • File

Version History

1.0 (latest) Created 16th Jul 2024 at 14:09 by Helena Rasche

Added/updated 4 files


Open master b21be8f

2.0 (earliest) Created 25th Jun 2024 at 11:01 by Helena Rasche

Added/updated 4 files


Frozen 2.0 b9e8765
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
SAMtools
seqtk
Unicycler
Bandage
fastp
NanoPlot
Minimap2
MultiQC
Bowtie 2
License
Creative Commons Attribution 4.0 International
Activity

Views: 663   Downloads: 193

Created: 25th Jun 2024 at 11:01

Last updated: 25th Jun 2024 at 11:01

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Total size: 143 KB
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