ERGA ONT+Illumina Assembly+QC NextDenovo+HyPo v2403 (WF2) Version 1
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Run on GalaxyThe workflow takes raw ONT reads and trimmed Illumina WGS paired reads collections, the ONT raw stats table (calculated from WF1) and the estimated genome size (calculated from WF1) to run NextDenovo and subsequently polish the assembly with HyPo. It produces collapsed assemblies (unpolished and polished) and runs all the QC analyses (gfastats, BUSCO, and Merqury).
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Estimated genome size | Estimated genome size | n/a |
|
| Illumina trimmed reads | Illumina trimmed reads | n/a |
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| Max depth | Max depth | n/a |
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| ONT raw stats table | ONT raw stats table | n/a |
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| ONT reads | ONT reads | fastq file with ONT reads |
|
| lineage | lineage | lineage for BUSCO, e.g.: arthropoda_odb10, vertebrata_odb10, mammalia_odb10... |
|
| meryl db | meryl db | import meryldb to run merqury on the assemblies obtained |
|
Steps
| ID | Name | Description |
|---|---|---|
| 7 | Datamash | toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0 |
| 8 | Parse parameter value | param_value_from_file |
| 9 | Parse parameter value | param_value_from_file |
| 10 | Flatten collection | __FLATTEN__ |
| 11 | Parse parameter value | param_value_from_file |
| 12 | Arithmetic Operations | toolshed.g2.bx.psu.edu/repos/devteam/tables_arithmetic_operations/tables_arithmetic_operations/1.0.0 |
| 13 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
| 14 | Parse parameter value | param_value_from_file |
| 15 | NextDenovo | toolshed.g2.bx.psu.edu/repos/bgruening/nextdenovo/nextdenovo/2.5.0+galaxy0 |
| 16 | Bandage Image | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
| 17 | GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
| 18 | gfastats nextdenovo | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
| 19 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0 |
| 20 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0 |
| 21 | BUSCO nextdenovo | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0 |
| 22 | Merqury nextdenovo | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2 |
| 23 | Merge BAM Files | toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0 |
| 24 | HyPo | toolshed.g2.bx.psu.edu/repos/iuc/hypo/hypo/1.0.3+galaxy0 |
| 25 | Merqury Hypo | merqury on flye assembly polished with 1 round of hypo toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2 |
| 26 | BUSCO Hypo | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0 |
| 27 | gfastats Hypo | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| _anonymous_output_1 | _anonymous_output_1 | n/a |
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| _anonymous_output_2 | _anonymous_output_2 | n/a |
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| _anonymous_output_3 | _anonymous_output_3 | n/a |
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| Map with minimap2 on input dataset(s) (mapped reads in BAM format) | Map with minimap2 on input dataset(s) (mapped reads in BAM format) | n/a |
|
| _anonymous_output_4 | _anonymous_output_4 | n/a |
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| _anonymous_output_5 | _anonymous_output_5 | n/a |
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| _anonymous_output_6 | _anonymous_output_6 | n/a |
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| Busco on input dataset(s): short summary | Busco on input dataset(s): short summary | n/a |
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| Merqury on input dataset(s): stats | Merqury on input dataset(s): stats | n/a |
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| QV stats | QV stats | n/a |
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| Merqury on input dataset(s): plots | Merqury on input dataset(s): plots | n/a |
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| HyPo on input dataset(s): polished assembly | HyPo on input dataset(s): polished assembly | n/a |
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| _anonymous_output_7 | _anonymous_output_7 | n/a |
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| _anonymous_output_8 | _anonymous_output_8 | n/a |
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| _anonymous_output_9 | _anonymous_output_9 | n/a |
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| _anonymous_output_10 | _anonymous_output_10 | n/a |
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| _anonymous_output_11 | _anonymous_output_11 | n/a |
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| _anonymous_output_12 | _anonymous_output_12 | n/a |
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| _anonymous_output_13 | _anonymous_output_13 | n/a |
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| _anonymous_output_14 | _anonymous_output_14 | n/a |
|
Version History
Version 1 (earliest) Created 11th Mar 2024 at 14:45 by Diego De Panis
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Views: 4790 Downloads: 596 Runs: 1
Created: 11th Mar 2024 at 14:45
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https://orcid.org/0000-0002-3679-9585
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, ERGA Analysis
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 de-novo genome assembly workflows written for implementation in Galaxy
Input data should be Oxford Nanopore raw reads plus Illumina WGS reads and Illumina 3-dimensional Chromatin Confirmation Capture (HiC) reads
Executing all workflows will output one scaffolded collapsed assembly and the complete QC analyses
Please run the workflows in order: WF0 (there are two, one for ONT, and another one for Illumina that can be used independently for the WGS and HiC reads), WF1, WF2, WF3, WF4
Maintainers: Diego De Panis
Number of items: 6
Tags: Assembly, Bioinformatics, Galaxy, Genomics, Genome assembly, ONT, illumina, Hi-C
