Galaxy Workflow ERGA-BGE Genome Report ASM analyses (one-asm Long Reads + HiC)
Version 1.1 (latest)

Version 1.1 (latest)

Version 1 (earliest)

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Workflow Type: Galaxy

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Assembly Evaluation for ERGA-BGE Reports

One Assembly, HiFi WGS reads + HiC reads

The workflow requires the following:

Species Taxonomy ID number
NCBI Genome assembly accession code
BUSCO Lineage
WGS accurate reads accession code
NCBI HiC reads accession code

The workflow will get the data and process it to generate genome profiling (genomescope, smudgeplot -optional-), assembly stats (gfastats), merqury stats (QV, completeness), BUSCO, snailplot, contamination blobplot, and HiC heatmap.

Use this workflow for HiFi- or ONT-based assemblies

SEEK ID: https://workflowhub.eu/workflows/1104?version=2

Inputs

ID	Name	Description	Type
BUSCO Lineage	BUSCO Lineage	n/a	string
MAPQ	MAPQ	n/a	int
Multiple Long Reads files?	Multiple Long Reads files?	IMPORTANT! If you entered more than one accession code, select Yes	boolean
NCBI Genome assembly accession code	NCBI Genome assembly accession code	Should start with GCA or GCF, e.g.: GCA_963556495.2	string
NCBI HiC reads accession code	NCBI HiC reads accession code	Comma-separated accession code of the reads. Must start with SRR, DRR or ERR, e.g. SRR925743, ERR343809	string
NCBI Long reads accession code	NCBI Long reads accession code	Comma-separated accession code of the reads. Must start with SRR, DRR or ERR, e.g. SRR925743, ERR343809	string
Ploidy	Ploidy	Default value: 2	int
Run Smudgeplot?	Run Smudgeplot?	n/a	boolean
Species Taxonomy ID number	Species Taxonomy ID number	Get the NCBI taxonomy number here: https://www.ncbi.nlm.nih.gov/taxonomy	int
The Long Reads are ONT	The Long Reads are ONT	n/a	boolean
The Long Reads are PacBio HiFi	The Long Reads are PacBio HiFi	n/a	boolean
kmer length	kmer length	Default value: 31	int

Steps

ID	Name	Description
1	taxdump address	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy3
13	downloads	lftp
14	NCBI Datasets Genomes	toolshed.g2.bx.psu.edu/repos/iuc/ncbi_datasets/datasets_download_genome/18.29.1+galaxy0
15	Faster Download and Extract Reads in FASTQ	toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1
16	Faster Download and Extract Reads in FASTQ	toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1
17	Collapse Collection	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
18	Flatten collection	__FLATTEN__
19	Meryl	toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6
20	Unzip collection	__UNZIP_COLLECTION__
21	Extract dataset	__EXTRACT_DATASET__
22	Meryl	toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6
23	Collapse Collection	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
24	Collapse Collection	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
25	gfastats	toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy2
26	Busco	toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy2
27	Diamond	toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.1.25+galaxy0
28	Create BlobtoolKit	toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/4.5.3+galaxy0
29	Map with minimap2	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.31+galaxy0
30	Map with minimap2	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.31+galaxy0
31	Convert FASTA to fai file	CONVERTER_fasta_to_fai
32	Meryl	toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6
33	Merqury	toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4
34	Zip collections	__ZIP_COLLECTION__
35	Sambamba merge	toolshed.g2.bx.psu.edu/repos/bgruening/sambamba_merge/sambamba_merge/1.0.1+galaxy2
36	Extract dataset	__EXTRACT_DATASET__
37	Sambamba merge	toolshed.g2.bx.psu.edu/repos/bgruening/sambamba_merge/sambamba_merge/1.0.1+galaxy2
38	Extract dataset	__EXTRACT_DATASET__
39	Cut	Cut1
40	Smudgeplot	toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/0.2.5+galaxy3
41	GenomeScope	toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.1.0+galaxy0
42	chromap	toolshed.g2.bx.psu.edu/repos/iuc/chromap/chromap/0.3.2+galaxy0
43	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
44	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
45	bedtools MakeWindowsBed	toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.31.1+galaxy0
46	cooler csort with tabix	toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.9.3+galaxy1
47	Sambamba flagstat	toolshed.g2.bx.psu.edu/repos/bgruening/sambamba_flagstat/sambamba_flagstat/1.0.1+galaxy2
48	Create BlobtoolKit 2	toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/4.5.3+galaxy0
49	Sambamba flagstat	toolshed.g2.bx.psu.edu/repos/bgruening/sambamba_flagstat/sambamba_flagstat/1.0.1+galaxy2
50	Create BlobtoolKit 3	toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/4.5.3+galaxy0
51	cooler_cload_tabix	toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.3+galaxy1
52	BlobToolKit	toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/4.5.3+galaxy0
53	BlobToolKit	toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/4.5.3+galaxy0
54	hicMergeMatrixBins	toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicmergematrixbins/hicexplorer_hicmergematrixbins/3.7.6+galaxy1
55	hicMergeMatrixBins	toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicmergematrixbins/hicexplorer_hicmergematrixbins/3.7.6+galaxy1
56	hicMergeMatrixBins	toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicmergematrixbins/hicexplorer_hicmergematrixbins/3.7.6+galaxy1
57	hicPlotMatrix	toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/3.7.6+galaxy1
58	hicPlotMatrix	toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/3.7.6+galaxy1
59	hicPlotMatrix	toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/3.7.6+galaxy1