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
Inputs
ID | Name | Description | Type |
---|---|---|---|
BUSCO Lineage | BUSCO Lineage | Choose the (eukaryotic) BUSCO lineage that corresponds to the assembled species, e.g.: mammalia_odb10 |
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Multiple HiC paired-end files? | Multiple HiC paired-end files? | IMPORTANT! If you entered more than one accession code, select Yes |
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NCBI Genome assembly accession code | NCBI Genome assembly accession code | Should start with GCA or GCF, e.g.: GCA_963556495.2 |
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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 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 |
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Ploidy | Ploidy | Default value: 2 |
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Run Smudgeplot? | Run Smudgeplot? | n/a |
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Species Taxonomy ID number | Species Taxonomy ID number | Get the NCBI taxonomy number here: https://www.ncbi.nlm.nih.gov/taxonomy |
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kmer length | kmer length | Default value: 21 |
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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 |
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Busco on input dataset(s): short summary | Busco on input dataset(s): short summary | n/a |
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Busco on input dataset(s): full table | Busco on input dataset(s): full table | n/a |
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Version History
Version 1.2 (latest) Created 4th Nov 2024 at 14:27 by Diego De Panis
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Version 1.1 Created 19th Aug 2024 at 13:35 by Diego De Panis
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Version-1.1
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Version 1 (earliest) Created 19th Aug 2024 at 10:38 by Diego De Panis
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Additional credit
ERGA
Submitter
Views: 909 Downloads: 115 Runs: 19
Created: 19th Aug 2024 at 10:38
Last updated: 20th Aug 2024 at 14:20
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