ERGA Long reads+HiC Assembly+QC Hifiasm v2602 (WF2)

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Workflow Type: Galaxy
Stable

The workflow takes a trimmed long reads collection, and Forward/Reverse HiC reads to run Hifiasm in HiC phasing mode. It produces both Pri/Alt and Hap1/Hap2 assemblies, and runs all the QC analysis (gfastats, BUSCO, and Merqury). The default Hifiasm purge level is aggressive (l3).

SEEK ID: https://workflowhub.eu/workflows/605?version=2

Inputs

ID Name Description Type
(Trimmed) Long Reads Collection (Trimmed) Long Reads Collection Collection of Long reads in fastq format
  • File[]
Estimated genome size Estimated genome size Select the est_genome_size result obtained during profiling
  • File
HiC F trimmed HiC F trimmed n/a
  • File
HiC R trimmed HiC R trimmed n/a
  • File
Meryl Database Meryl Database Select the meryl_db result obtained during profiling
  • File
The Long Reads are PacBio HiFi The Long Reads are PacBio HiFi If your long reads are HiFi, leave it 'yes'
  • boolean
The Long reads are ONT The Long reads are ONT If your long reads are ONT, switch to 'yes'. IMPORTANT: Remember to also switch HiFi to 'no'
  • boolean
lineage lineage lineage for BUSCO, e.g.: arthropoda_odb10, vertebrata_odb10, mammalia_odb10, aves_odb10, tetrapoda_odb10 ...
  • string

Steps

ID Name Description
8 Hifiasm toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.25.0+galaxy1
9 Hifiasm toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.25.0+galaxy1
10 Parse parameter value param_value_from_file
11 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
12 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
13 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
14 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
15 GFA to FASTA toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
16 Bandage Pri toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
17 gfastats pri toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
18 GFA to FASTA toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
19 Bandage alt toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
20 gfastats alt toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
21 GFA to FASTA toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
22 Bandage Hap1 toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
23 gfastats Hap1 toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
24 GFA to FASTA toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2
25 Bandage Hap2 toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
26 gfastats Hap2 toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
27 BUSCO pri toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy2
28 BUSCO alt toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy2
29 Merqury pri/alt toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4
30 BUSCO Hap1 toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy2
31 BUSCO Hap2 toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy2
32 Merqury Hap1/Hap2 toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4

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
_anonymous_output_5 _anonymous_output_5 n/a
  • File
_anonymous_output_6 _anonymous_output_6 n/a
  • File
_anonymous_output_7 _anonymous_output_7 n/a
  • File
_anonymous_output_8 _anonymous_output_8 n/a
  • File
_anonymous_output_9 _anonymous_output_9 n/a
  • File
_anonymous_output_10 _anonymous_output_10 n/a
  • File
_anonymous_output_11 _anonymous_output_11 n/a
  • File
_anonymous_output_12 _anonymous_output_12 n/a
  • File
_anonymous_output_13 _anonymous_output_13 n/a
  • File
_anonymous_output_14 _anonymous_output_14 n/a
  • File
_anonymous_output_15 _anonymous_output_15 n/a
  • File
_anonymous_output_16 _anonymous_output_16 n/a
  • File
_anonymous_output_17 _anonymous_output_17 n/a
  • File
_anonymous_output_18 _anonymous_output_18 n/a
  • File
_anonymous_output_19 _anonymous_output_19 n/a
  • File
_anonymous_output_20 _anonymous_output_20 n/a
  • File
_anonymous_output_21 _anonymous_output_21 n/a
  • File
_anonymous_output_22 _anonymous_output_22 n/a
  • File

Version History

Version 2 (latest) Created 11th Feb 2026 at 20:03 by Diego De Panis

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Open master 63c4f4b

Version 1 (earliest) Created 9th Oct 2023 at 13:47 by Diego De Panis

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https://github.com/ERGA-consortium/pipelines/discussions
License
MIT License (MIT)
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Views: 8335   Downloads: 748   Runs: 13

Created: 9th Oct 2023 at 13:47

Last updated: 11th Feb 2026 at 20:05

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