Post-assembly workflow

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Workflow Type: Galaxy

ERGA post-assembly QC

Associated Tutorial

This workflows is part of the tutorial ERGA post-assembly QC, available in the GTN

Features

Thanks to...

Workflow Author(s): Cristóbal Gallardo Alba

Tutorial Author(s): Fabian Recktenwald, Cristóbal Gallardo, Tom Brown

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1127?version=3

Inputs

ID Name Description Type
DIAMOND database DIAMOND database n/a
  • File
Hi-C forward Hi-C forward n/a
  • File[]
Hi-C reverse Hi-C reverse n/a
  • File[]
Long-read FASTQ files Long-read FASTQ files n/a
  • File[]
Metadata file Metadata file n/a
  • File?
NCBI taxdump directory NCBI taxdump directory n/a
  • File
NCBI taxonomic ID NCBI taxonomic ID n/a
  • int
Ploidy for model to use Ploidy for model to use n/a
  • int?
Primary genome assembly file (fasta) Primary genome assembly file (fasta) n/a
  • File

Steps

ID Name Description
9 Meryl toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6
10 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
11 Create BlobtoolKit toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/4.0.7+galaxy2
12 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.2.0+galaxy0
13 Convert compressed file to uncompressed. CONVERTER_gz_to_uncompressed
14 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
15 Diamond toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0
16 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
17 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
18 Meryl toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6
19 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0
20 Smudgeplot toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/0.2.5+galaxy+2
21 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4
22 Bandage Image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
23 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0
24 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0
25 Merqury toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2
26 Meryl toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6
27 Samtools stats toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.4
28 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.4+galaxy0
29 Filter and merge toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy0
30 Merqury plot 2 __EXTRACT_DATASET__
31 Merqury plot 1 __EXTRACT_DATASET__
32 Merqury plot 3 __EXTRACT_DATASET__
33 Merqury plot 5 __EXTRACT_DATASET__
34 Merqury plot 4 __EXTRACT_DATASET__
35 GenomeScope toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2
36 BlobToolKit toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/4.0.7+galaxy2
37 PretextMap toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0
38 BlobToolKit toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/4.0.7+galaxy2
39 BlobToolKit toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/4.0.7+galaxy2
40 BlobToolKit toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/4.0.7+galaxy2
41 Pretext Snapshot toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+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
Merqury on input dataset(s): stats Merqury on input dataset(s): stats n/a
  • File
Merqury on input dataset(s): plots Merqury on input dataset(s): plots n/a
  • File
Merqury on input dataset(s): QV stats Merqury on input dataset(s): QV stats n/a
  • File
_anonymous_output_7 _anonymous_output_7 n/a
  • File
Busco on input dataset(s): full table Busco on input dataset(s): full table n/a
  • File
Busco on input dataset(s): short summary Busco on input dataset(s): short summary 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

Version History

2.0 (latest) Created 9th Sep 2024 at 14:24 by Helena Rasche

Added/updated 4 files


Open master 1553de1

1.0 Created 16th Jul 2024 at 14:08 by Helena Rasche

Added/updated 4 files


Frozen 1.0 b156a44

3.0 (earliest) Created 25th Jun 2024 at 11:00 by Helena Rasche

Added/updated 4 files


Frozen 3.0 1329bf0
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
gfastats
Diamond
Smudgeplots
Bandage
Bwa-mem2
Merqury
SAMtools
BUSCO
GenomeScope 2.0
Minimap2
License
GNU Affero General Public License v3.0 or later
Activity

Views: 755   Downloads: 266

Created: 25th Jun 2024 at 11:00

Last updated: 9th Sep 2024 at 14:24

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Total size: 286 KB
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