ERGA ONT+Illumina Assembly+QC Flye+HyPo v2403 (WF2)
Version 1

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Run on Galaxy

Workflow Type: Galaxy

Stable

The workflow takes raw ONT reads and trimmed Illumina WGS paired reads collections, and the estimated genome size and Max depth (both calculated from WF1) to run Flye and subsequently polish the assembly with HyPo. It produces collapsed assemblies (unpolished and polished) and runs all the QC analyses (gfastats, BUSCO, and Merqury).

SEEK ID: https://workflowhub.eu/workflows/788?version=1

Inputs

ID	Name	Description	Type
Estimated genome size	Estimated genome size	n/a	File
Illumina trimmed reads	Illumina trimmed reads	n/a	File[]
Max depth	Max depth	n/a	File
ONT reads	ONT reads	fastq file with ONT reads	File
lineage	lineage	lineage for BUSCO, e.g.: arthropoda_odb10, vertebrata_odb10, mammalia_odb10...	string
meryl db	meryl db	import meryldb to run merqury on the assemblies obtained	File

Steps

ID	Name	Description
6	Flatten collection	__FLATTEN__
7	Flye	toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0
8	Parse parameter value	param_value_from_file
9	Parse parameter value	param_value_from_file
10	Parse parameter value	param_value_from_file
11	BWA-MEM2	toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0
12	Map with minimap2	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0
13	Bandage Image	toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
14	BUSCO flye	toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0
15	Merqury flye	toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2
16	gfastats flye	toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
17	Merge BAM Files	toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0
18	HyPo	toolshed.g2.bx.psu.edu/repos/iuc/hypo/hypo/1.0.3+galaxy0
19	Merqury Hypo	merqury on flye assembly polished with 1 round of hypo toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2
20	gfastats Hypo	toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
21	BUSCO Hypo	toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0

Outputs

ID	Name	Description	Type
consensus	consensus	n/a	File
assembly_gfa	assembly_gfa	n/a	File
_anonymous_output_1	_anonymous_output_1	n/a	File
Map with minimap2 on input dataset(s) (mapped reads in BAM format)	Map with minimap2 on input dataset(s) (mapped reads in BAM format)	n/a	File
_anonymous_output_2	_anonymous_output_2	n/a	File
Busco on input dataset(s): short summary	Busco on input dataset(s): short summary	n/a	File
_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
Merqury on input dataset(s): plots	Merqury on input dataset(s): plots	n/a	File
QV stats	QV stats	n/a	File
Merqury on input dataset(s): stats	Merqury on input dataset(s): stats	n/a	File
_anonymous_output_6	_anonymous_output_6	n/a	File
output1	output1	n/a	File
HyPo on input dataset(s): polished assembly	HyPo on input dataset(s): polished assembly	n/a	File
_anonymous_output_7	_anonymous_output_7	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
_anonymous_output_13	_anonymous_output_13	n/a	File
_anonymous_output_14	_anonymous_output_14	n/a	File