Workflow Type: Galaxy
Open
Frozen
Stable
The workflow takes trimmed HiC paired-end reads collection, and Pri/Alt assemblies to produce a scaffolded primary assembly (and alternate contigs) using YaHS. It also runs Pretext and all the QC analyses (gfastats, BUSCO, and Merqury).
Inputs
ID | Name | Description | Type |
---|---|---|---|
(Trimmed) Hi-C Reads | (Trimmed) Hi-C Reads | Collection of Hi-C reads in fastq format |
|
Alt (Purged) Contigs GFA | Alt (Purged) Contigs GFA | Alternate contigs in GFA format from the Purge_Dups run results: alt_purged_gfa |
|
Estimated genome size | Estimated genome size | Select the est_genome_size result obtained during profiling |
|
Lineage | Lineage | lineage for BUSCO, e.g.: arthropoda_odb10, vertebrata_odb10, mammalia_odb10, aves_odb10, tetrapoda_odb10 ... |
|
Meryl database | Meryl database | Select the meryl_db result obtained during profiling |
|
Multiple Hi-C paired-end files? | Multiple Hi-C paired-end files? | IMPORTANT! If you have more than one pair of paired-end files, select Yes |
|
Pri (Purged) Contigs GFA | Pri (Purged) Contigs GFA | Primary contigs in GFA format from the Purge_Dups run results: pri_purged_gfa |
|
Steps
ID | Name | Description |
---|---|---|
7 | GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
8 | GFA to FASTA | toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2 |
9 | Parse parameter value | param_value_from_file |
10 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy4 |
11 | Convert FASTA to fai file | CONVERTER_fasta_to_fai |
12 | Extract dataset | __EXTRACT_DATASET__ |
13 | Sambamba merge | toolshed.g2.bx.psu.edu/repos/bgruening/sambamba_merge/sambamba_merge/1.0.1+galaxy2 |
14 | Cut | Cut1 |
15 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
16 | Sambamba flagstat | toolshed.g2.bx.psu.edu/repos/bgruening/sambamba_flagstat/sambamba_flagstat/1.0.1+galaxy1 |
17 | Pairtools parse | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_parse/pairtools_parse/1.1.3+galaxy0 |
18 | Pairtools sort | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_sort/pairtools_sort/1.1.3+galaxy0 |
19 | Pairtools dedup | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_dedup/pairtools_dedup/1.1.3+galaxy0 |
20 | Pairtools split | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_split/pairtools_split/1.1.3+galaxy0 |
21 | PretextMap | toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1 |
22 | YAHS | toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy2 |
23 | Pretext Snapshot | toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0 |
24 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0 |
25 | Convert FASTA to fai file | CONVERTER_fasta_to_fai |
26 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy4 |
27 | Merqury | toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4 |
28 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1 |
29 | Cut | Cut1 |
30 | Extract dataset | __EXTRACT_DATASET__ |
31 | Sambamba merge | toolshed.g2.bx.psu.edu/repos/bgruening/sambamba_merge/sambamba_merge/1.0.1+galaxy2 |
32 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
33 | Sambamba flagstat | toolshed.g2.bx.psu.edu/repos/bgruening/sambamba_flagstat/sambamba_flagstat/1.0.1+galaxy1 |
34 | Pairtools parse | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_parse/pairtools_parse/1.1.3+galaxy0 |
35 | Pairtools sort | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_sort/pairtools_sort/1.1.3+galaxy0 |
36 | Pairtools dedup | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_dedup/pairtools_dedup/1.1.3+galaxy0 |
37 | Pairtools split | toolshed.g2.bx.psu.edu/repos/iuc/pairtools_split/pairtools_split/1.1.3+galaxy0 |
38 | PretextMap | toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1 |
39 | Pretext Snapshot | toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
_anonymous_output_1 | _anonymous_output_1 | n/a |
|
_anonymous_output_2 | _anonymous_output_2 | n/a |
|
_anonymous_output_3 | _anonymous_output_3 | n/a |
|
_anonymous_output_4 | _anonymous_output_4 | n/a |
|
parsed_pairs_stats | parsed_pairs_stats | n/a |
|
dedup_pairs_stats | dedup_pairs_stats | n/a |
|
Version History
Version 2 (latest) Created 3rd Feb 2025 at 13:07 by Diego De Panis
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Version 1 (earliest) Created 24th Sep 2024 at 22:54 by Diego De Panis
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Created: 24th Sep 2024 at 22:54
Last updated: 1st Jun 2025 at 12:05
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