annotation_helixer

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Workflow Type: Galaxy

Structural genome annotation with Helixer

Associated Tutorial

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

Features

Thanks to...

Workflow Author(s): Romane Libouban

Tutorial Author(s): Romane LIBOUBAN, Anthony Bretaudeau

Funder(s): EuroScienceGateway

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1358?version=1

Inputs

ID Name Description Type
Genome #main/Genome Genome input (fasta format)
  • File

Steps

ID Name Description
1 Helixer Structural annotation step toolshed.g2.bx.psu.edu/repos/genouest/helixer/helixer/0.3.3+galaxy1
2 compleasm Compleam is described as a faster and more accurate reimplementation of Busco. toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.5+galaxy0
3 BUSCO BSUCO assesses the quality of genomic data. The tool inspects the transcription sequences of predicted genes. toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0
4 Genome annotation statistics Helixer Calculate statistics from a genome annotation in GFF3 format toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4
5 JBrowse Visualization toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1

Outputs

ID Name Description Type
BUSCO gff3 #main/BUSCO gff3 n/a
  • File
BUSCO miniprot #main/BUSCO miniprot n/a
  • File
BUSCO missing #main/BUSCO missing n/a
  • File
BUSCO sum #main/BUSCO sum n/a
  • File
BUSCO summary image #main/BUSCO summary image n/a
  • File
BUSCO table #main/BUSCO table n/a
  • File
Helixer #main/Helixer n/a
  • File
JBrowse output #main/JBrowse output n/a
  • File
compleasm full table #main/compleasm full table n/a
  • File
compleasm full table busco #main/compleasm full table busco n/a
  • File
compleasm miniprot #main/compleasm miniprot n/a
  • File
compleasm translated protein #main/compleasm translated protein n/a
  • File
graphs helixer #main/graphs helixer n/a
  • File
summary helixer #main/summary helixer n/a
  • File

Version History

2.0 (latest) Created 9th Dec 2024 at 13:45 by Helena Rasche

Added/updated 4 files


Open master 64dfadc

1.0 (earliest) Created 26th Aug 2024 at 14:08 by Helena Rasche

Added/updated 4 files


Frozen 1.0 6340b35
help Creators and Submitter
Creators
Not specified
Submitter
Tools
Helixer
BUSCO
JBrowse
gffread
OMArk
License
MIT License (MIT)
Activity

Views: 1315   Downloads: 524   Runs: 0

Created: 26th Aug 2024 at 14:08

Last updated: 9th Dec 2024 at 13:45

help Attributions

None

Total size: 95 KB
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