Workflow Type: Galaxy
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
  • File[]
Alt (Purged) Contigs GFA Alt (Purged) Contigs GFA Alternate contigs in GFA format from the Purge_Dups run results: alt_purged_gfa
  • File
Estimated genome size Estimated genome size Select the est_genome_size result obtained during profiling
  • File
Lineage Lineage lineage for BUSCO, e.g.: arthropoda_odb10, vertebrata_odb10, mammalia_odb10, aves_odb10, tetrapoda_odb10 ...
  • string
Meryl database Meryl database Select the meryl_db result obtained during profiling
  • File
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
  • boolean
Pri (Purged) Contigs GFA Pri (Purged) Contigs GFA Primary contigs in GFA format from the Purge_Dups run results: pri_purged_gfa
  • File

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
  • File
_anonymous_output_2 _anonymous_output_2 n/a
  • File
_anonymous_output_3 _anonymous_output_3 n/a
  • File
_anonymous_output_4 _anonymous_output_4 n/a
  • File
parsed_pairs_stats parsed_pairs_stats n/a
  • File
dedup_pairs_stats dedup_pairs_stats n/a
  • File

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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