ERGA-BGE Genome Report ASM analyses (one-asm HiFi + HiC)
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Run on GalaxyAssembly 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-based assemblies where the WGS accurate reads are PacBio HiFi
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| BUSCO Lineage | BUSCO Lineage | Choose the (eukaryotic) BUSCO lineage that corresponds to the assembled species, e.g.: mammalia_odb10 |
|
| Multiple HiC paired-end files? | Multiple HiC paired-end files? | IMPORTANT! If you entered more than one accession code, select Yes |
|
| NCBI Genome assembly accession code | NCBI Genome assembly accession code | Should start with GCA or GCF, e.g.: GCA_963556495.2 |
|
| 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 |
|
| 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 |
|
| Ploidy | Ploidy | Default value: 2 |
|
| Run Smudgeplot? | Run Smudgeplot? | n/a |
|
| Species Taxonomy ID number | Species Taxonomy ID number | Get the NCBI taxonomy number here: https://www.ncbi.nlm.nih.gov/taxonomy |
|
| kmer length | kmer length | Default value: 21 |
|
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 |
|
| Busco on input dataset(s): full table | Busco on input dataset(s): full table | n/a |
|
Version History
Version 1.1 (latest) Created 4th Nov 2024 at 14:29 by Diego De Panis
Open
master9b0d0d4
Version 1 (earliest) Created 20th Aug 2024 at 14:19 by Diego De Panis
Initial commit
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Creators and SubmitterViews: 1111 Downloads: 134 Runs: 32
Created: 20th Aug 2024 at 14:19
Last updated: 5th Dec 2024 at 16:47
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Teams: ERGA Assembly
Organizations: IZW
Welcome to the ERGA Space!
Here we collect, curate and develop pipelines to assemble and annotation reference-quality genomes for all eukaryotic life.
For Genome Assembly pipelines head to our Assembly Team
For Genome Annotation pipelines head to our Annotation Team
Development, discussions and issue tracking takes place in the ERGA github repo
If you would like to join ...
Teams: ERGA Assembly, ERGA Annotation
Web page: https://www.erga-biodiversity.eu/
A collection of workflows and pipelines developed as part of the ERGA consortium
Space: ERGA
Public web page: https://www.erga-biodiversity.eu/
Collection of Galaxy workflows for generating results used for creating ERGA-BGE Reports
For a given genome, two workflows should be run: the assembly evaluation (ASM analyses), and the annotation evaluation (ANNOT analyses)
Depending on the kind of data used for the genome assembly, you should choose HiFi or ONT (Illumina) workflows for ASM analyses
