VGP assembly: training workflow

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Workflow Type: Galaxy

VGP assembly tutorial

Associated Tutorial

This workflows is part of the tutorial VGP assembly: training workflow, available in the GTN

Thanks to...

Tutorial Author(s): Delphine Lariviere, Alex Ostrovsky, Cristóbal Gallardo, Anna Syme, Linelle Abueg, Brandon Pickett, Giulio Formenti, Marcella Sozzoni, Anton Nekrutenko

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1187?version=2

Inputs

ID Name Description Type
Bionano_dataset Bionano_dataset n/a
  • File
Hi-C_dataset_F Hi-C_dataset_F n/a
  • File
Hi-C_dataset_R Hi-C_dataset_R n/a
  • File
Input Dataset Collection Input Dataset Collection n/a
  • File[]

Steps

ID Name Description
4 GFA to FASTA toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
5 GFA to FASTA toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
6 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy2
7 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2
8 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2
9 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy4
10 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
11 Meryl toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy4
12 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0
13 Quast toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy4
14 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0
15 Meryl toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy4
16 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy4
17 Meryl toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy4
18 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy1
19 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy4
20 GenomeScope toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy1
21 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy4
22 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
23 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6
24 Bionano Hybrid Scaffold toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy0
25 Concatenate datasets cat1
26 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2
27 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
28 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6
29 Concatenate datasets cat1
30 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy4
31 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0
32 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
33 Advanced Cut toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0
34 Advanced Cut toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0
35 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0
36 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0
37 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
38 Quast toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy4
39 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2
40 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0
41 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy4
42 Convert Convert characters1
43 Filter and merge toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy0
44 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy4
45 Advanced Cut toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0
46 bedtools BAM to BED toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2
47 PretextMap toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0
48 Purge overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy4
49 Sort sort1
50 Pretext Snapshot toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1
51 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2
52 Quast toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy4
53 SALSA toolshed.g2.bx.psu.edu/repos/iuc/salsa/salsa/2.3+galaxy2
54 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0
55 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0
56 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2
57 Quast toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy4
58 Filter and merge toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy0
59 PretextMap toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0
60 Pretext Snapshot toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1

Version History

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

Added/updated 4 files


Open master 1daad4b

8.0 (earliest) Created 25th Jun 2024 at 11:07 by Helena Rasche

Added/updated 4 files


Frozen 8.0 8b7fbbe
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
Cutadapt
BUSCO
purge_dups
Minimap2
QUAST
Merqury
GenomeScope 2.0
Bwa-mem2
BEDTools
SALSA
License
Creative Commons Attribution 4.0 International
Activity

Views: 644   Downloads: 215

Created: 25th Jun 2024 at 11:07

Last updated: 25th Jun 2024 at 11:07

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