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

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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=1

DOI: 10.48546/workflowhub.workflow.1103.1

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 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

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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.1103.1
License
MIT License (MIT)
Activity

Views: 4983   Downloads: 999   Runs: 50

Created: 19th Aug 2024 at 10:38

Last updated: 5th Dec 2024 at 16:48

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