annotation-maker/main
v0.1

Workflow Type: Galaxy

This workflow allows for genome annotation using Maker and evaluates the quality of the annotation.

SEEK ID: https://workflowhub.eu/workflows/1323?version=1

DOI: 10.48546/workflowhub.workflow.1323.1

Inputs

ID	Name	Description	Type
Augustus training	Augustus training	Augustus training	File
BUSCO lineage	BUSCO lineage	BUSCO lineage	string
Genome assembly	Genome assembly	Genome assembly	File
Genome sequence	Genome sequence	Genome sequence	File
Protein sequences	Protein sequences	Protein sequences	File
SNAP training	SNAP training	SNAP training	File

ID	Name	Description
6	Fasta Statistics	Fasta Statistics on the genome toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0
7	BUSCO on the genome sequences	Completeness assessment of the genome using the Busco tool toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0
8	Maker	Annotation with Maker toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.11+galaxy2
9	GFFRead	toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0
10	Genome annotation statistics	Genome annotation statistics on the maker's annotation toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4
11	Map annotation ids	toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11
12	BUSCO on the predicted protein sequences	Completeness assessment of the genome using the Busco tool toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0
13	JBrowse	toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1

ID	Name	Description	Type
fasta stats genome	fasta stats genome	n/a	File
busco image genome	busco image genome	n/a	File
busco sum genome	busco sum genome	n/a	File
busco table genome	busco table genome	n/a	File
busco gff genome	busco gff genome	n/a	File
busco missing genome	busco missing genome	n/a	File
maker full	maker full	n/a	File
maker gff	maker gff	n/a	File
maker evidences	maker evidences	n/a	File
gffread exons	gffread exons	n/a	File
graphs genome	graphs genome	n/a	File
summary genome	summary genome	n/a	File
renamed gff3	renamed gff3	n/a	File
id map	id map	n/a	File
busco missing predicted proteins	busco missing predicted proteins	n/a	File
busco table predicted proteins	busco table predicted proteins	n/a	File
busco gff predicted proteins	busco gff predicted proteins	n/a	File
busco sum predicted proteins	busco sum predicted proteins	n/a	File
busco image predicted proteins	busco image predicted proteins	n/a	File
jbrowse	jbrowse	n/a	File