ERGA-BGE Genome Report ASM analyses (one-asm HiFi + HiC)
Version 1 (earliest)

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 Assmebly, 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-based assemblies where the WGS accurate reads are PacBio HiFi

SEEK ID: https://workflowhub.eu/workflows/1104?version=1

DOI: 10.48546/workflowhub.workflow.1104.1

Inputs

ID	Name	Description	Type
BUSCO Lineage	BUSCO Lineage	Choose the (eukaryotic) BUSCO lineage that corresponds to the assembled species, e.g.: mammalia_odb10	string
Multiple HiC paired-end files?	Multiple HiC paired-end 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 HiFi reads accession code	NCBI HiFi 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
kmer length	kmer length	Default value: 21	int?

Steps

ID	Name	Description
1	taxdump address	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1
10	downloads	lftp
11	NCBI Datasets Genomes	toolshed.g2.bx.psu.edu/repos/iuc/ncbi_datasets/datasets_download_genome/16.20.0+galaxy0
12	Faster Download and Extract Reads in FASTQ	toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy0
13	Faster Download and Extract Reads in FASTQ	toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy0
14	Collapse Collection	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
15	Flatten collection	__FLATTEN__
16	Cutadapt	toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1
17	fastp	toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0
18	Extract dataset	__EXTRACT_DATASET__
19	Flatten collection	__FLATTEN__
20	Create BlobtoolKit	toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/4.0.7+galaxy2
21	gfastats	toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
22	Diamond	toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0
23	Map with minimap2	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0
24	Busco	toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0
25	BWA-MEM2	toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
26	Convert FASTA to fai file	CONVERTER_fasta_to_fai
27	Meryl	toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6
28	Merge BAM Files	toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0
29	Sambamba merge	toolshed.g2.bx.psu.edu/repos/bgruening/sambamba_merge/sambamba_merge/1.0.1+galaxy1
30	Extract dataset	__EXTRACT_DATASET__
31	Cut	Cut1
32	Meryl	toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6
33	BlobToolKit	toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/4.0.7+galaxy2
34	BAM/SAM Mapping Stats	toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/5.0.3+galaxy0
35	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
36	bedtools MakeWindowsBed	toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.31.1
37	Merqury	toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3
38	Meryl	toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6
39	BlobToolKit	toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/4.0.7+galaxy2
40	BlobToolKit	toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/4.0.7+galaxy2
41	Pairtools parse	toolshed.g2.bx.psu.edu/repos/iuc/pairtools_parse/pairtools_parse/1.1.0+galaxy1
42	Sambamba flagstat	toolshed.g2.bx.psu.edu/repos/bgruening/sambamba_flagstat/sambamba_flagstat/1.0.1+galaxy1
43	Smudgeplot	toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/0.2.5+galaxy3
44	GenomeScope	toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2
45	Pairtools sort	toolshed.g2.bx.psu.edu/repos/iuc/pairtools_sort/pairtools_sort/1.1.0+galaxy1
46	Pairtools dedup	toolshed.g2.bx.psu.edu/repos/iuc/pairtools_dedup/pairtools_dedup/1.1.0+galaxy1
47	Pairtools split	toolshed.g2.bx.psu.edu/repos/iuc/pairtools_split/pairtools_split/1.1.0+galaxy1
48	cooler csort with tabix	toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.8.11+galaxy1
49	cooler_cload_tabix	toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.8.11+galaxy1
50	hicMergeMatrixBins	toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicmergematrixbins/hicexplorer_hicmergematrixbins/3.7.2+galaxy0
51	hicMergeMatrixBins	toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicmergematrixbins/hicexplorer_hicmergematrixbins/3.7.2+galaxy0
52	hicPlotMatrix	toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/3.7.2+galaxy0
53	hicPlotMatrix	toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/3.7.2+galaxy0

Outputs

ID	Name	Description	Type
Busco on input dataset(s): short summary	Busco on input dataset(s): short summary	n/a	File
Busco on input dataset(s): full table	Busco on input dataset(s): full table	n/a	File