Genome annotation with Maker

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Workflow Type: Galaxy

Genome annotation with Maker

Associated Tutorial

This workflows is part of the tutorial Genome annotation with Maker , available in the GTN

Thanks to...

Tutorial Author(s): Anthony Bretaudeau

Workflow Author(s): Anthony Bretaudeau, French National Institute for Agriculture, Food, and Environment (INRAE)

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1164?version=2

Inputs

ID Name Description Type
or cDNA #main/EST and/or cDNA It contains the sequences used by Maker to construct gene models.
  • File
Genome sequence #main/Genome sequence This file corresponds to the sequence to be annotated.
  • File
Protein sequences #main/Protein sequences A set of protein sequences, usually from closely related species or from a curated sequence database like UniProt/SwissProt.
  • File

Steps

ID Name Description
3 Maker toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.11
4 Fasta Statistics toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1
5 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4
6 Train Augustus toolshed.g2.bx.psu.edu/repos/bgruening/augustus_training/augustus_training/3.3.3
7 Genome annotation statistics toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4
8 gffread toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2
9 Train SNAP toolshed.g2.bx.psu.edu/repos/iuc/snap_training/snap_training/2013_11_29+galaxy1
10 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4
11 Maker toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.11
12 gffread toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2
13 Train Augustus toolshed.g2.bx.psu.edu/repos/bgruening/augustus_training/augustus_training/3.3.3
14 Genome annotation statistics toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4
15 Train SNAP toolshed.g2.bx.psu.edu/repos/iuc/snap_training/snap_training/2013_11_29+galaxy1
16 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4
17 Maker toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.11
18 Map annotation ids toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11
19 JBrowse toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0
20 gffread toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2
21 Genome annotation statistics toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4
22 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4

Outputs

ID Name Description Type
trained model #main/ trained model n/a
  • File
full table #main/ full table n/a
  • File
list of missing ortholog genes #main/ list of missing ortholog genes n/a
  • File
short summary #main/ short summary n/a
  • File
Busco summary final round #main/Busco summary final round n/a
  • File
Busco summary first round #main/Busco summary first round n/a
  • File
Busco summary second round #main/Busco summary second round n/a
  • File
Fasta Statistics on input dataset(s): Fasta summary stats #main/Fasta Statistics on input dataset(s): Fasta summary stats n/a
  • File
Genome annotation statistics: graphs (first round) #main/Genome annotation statistics: graphs (first round) n/a
  • File
Genome annotation statistics: graphs (second round) #main/Genome annotation statistics: graphs (second round) n/a
  • File
Genome annotation statistics: graphs (third round) #main/Genome annotation statistics: graphs (third round) n/a
  • File
Genome annotation statistics: summary (first round) #main/Genome annotation statistics: summary (first round) n/a
  • File
Genome annotation statistics: summary (second round) #main/Genome annotation statistics: summary (second round) n/a
  • File
Genome annotation statistics: summary (third round) #main/Genome annotation statistics: summary (third round) n/a
  • File
cds #main/ cds n/a
  • File
exons #main/ exons n/a
  • File
translation of cds #main/ translation of cds n/a
  • File
report #main/ report n/a
  • File
Map annotation ids: renamed GFF #main/Map annotation ids: renamed GFF n/a
  • File
trained model #main/ trained model n/a
  • File

Version History

10.0 (latest) Created 16th Jul 2024 at 14:05 by Helena Rasche

Added/updated 4 files


Open master 6cda522

12.0 (earliest) Created 25th Jun 2024 at 11:05 by Helena Rasche

Added/updated 4 files


Frozen 12.0 1e59b0b
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
MAKER
BUSCO
AUGUSTUS
gffread
SNAP
JBrowse
License
GNU General Public License v3.0 or later
Activity

Views: 470   Downloads: 140

Created: 25th Jun 2024 at 11:05

Last updated: 25th Jun 2024 at 11:05

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