ERGA-BGE Genome Report ASM analyses (one-asm WGS Illumina PE + HiC)

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Workflow Type: Galaxy
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Assembly Evaluation for ERGA-BGE Reports

One Assmebly, Illumina 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 ONT-based assemblies where the WGS accurate reads are Illumina PE

SEEK ID: https://workflowhub.eu/workflows/1103?version=2

DOI: 10.48546/workflowhub.workflow.1103.2

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 Illumina WGS PE reads accession code NCBI Illumina WGS PE 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 fastp toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0
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+galaxy1
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 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
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+galaxy1
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

Version History

Version 1.2 (latest) Created 4th Nov 2024 at 14:27 by Diego De Panis

No revision comments

Open master a3102c4

Version 1.1 Created 19th Aug 2024 at 13:35 by Diego De Panis

No revision comments

Frozen Version-1.1 31ffcd1

Version 1 (earliest) Created 19th Aug 2024 at 10:38 by Diego De Panis

Initial commit


Frozen Version-1 f4998e3
help Creators and Submitter
Creator
Additional credit

ERGA

Submitter
Discussion Channel
https://github.com/ERGA-consortium/pipelines/discussions
Tools
NCBI Datasets
SRA Software Toolkit
fastp
gfastats
Diamond
Bwa-mem2
BUSCO
Picard
RSeQC
BEDTools
Merqury
Smudgeplots
GenomeScope 2.0
HiCExplorer
Citation
De Panis, D. (2024). ERGA-BGE Genome Report ASM analyses (one-asm WGS Illumina PE + HiC). WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.1103.2
License
MIT License
Activity

Views: 907   Downloads: 114   Runs: 19

Created: 19th Aug 2024 at 10:38

Last updated: 20th Aug 2024 at 14:20

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