assembly_with_preprocessing_and_sra_download

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Workflow Type: Galaxy

Assembly with preprocessing and SRA download

Associated Tutorial

This workflows is part of the tutorial assembly_with_preprocessing_and_sra_download, 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/1197?version=2

Inputs

ID Name Description Type
List of Illumina accessions List of Illumina accessions n/a
  • File
List of ONT accessions List of ONT accessions n/a
  • File

Steps

ID Name Description
10 Samtools stats toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
11 Samtools view toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1
12 Samtools fastx toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1
13 Samtools fastx toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1
14 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2
15 Zip Collection __ZIP_COLLECTION__
16 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2
17 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2
18 seqtk_sample toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2
19 seqtk_sample toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2
2 Illumina data toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1
20 Create assemblies with Unicycler toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0
21 Bandage Info toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1
22 Bandage Image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2
23 Filter sequences by length toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2
3 ONT data toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1
4 fastp: Trimmed Illumina Reads toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1
5 NanoPlot toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1
6 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1
7 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7
8 Bowtie2 toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0
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
_anonymous_output_19 _anonymous_output_19 n/a
  • File
_anonymous_output_20 _anonymous_output_20 n/a
  • File

Version History

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

Added/updated 4 files


Open master 112bb43

2.0 (earliest) Created 25th Jun 2024 at 11:08 by Helena Rasche

Added/updated 4 files


Frozen 2.0 ab99bf8
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
SAMtools
seqtk
SRA Software Toolkit
Unicycler
Bandage
fastp
NanoPlot
Minimap2
MultiQC
Bowtie 2
License
Creative Commons Attribution 4.0 International
Activity

Views: 626   Downloads: 214

Created: 25th Jun 2024 at 11:08

Last updated: 25th Jun 2024 at 11:08

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Total size: 141 KB
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