ERGA ONT+Illumina Assembly+QC Flye+HyPo v2403 (WF2)
Version 1

Workflow Type: Galaxy
Stable

The workflow takes raw ONT reads and trimmed Illumina WGS paired reads collections, and the estimated genome size and Max depth (both calculated from WF1) to run Flye 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
  • File
Illumina trimmed reads Illumina trimmed reads n/a
  • File[]
Max depth Max depth n/a
  • File
ONT reads ONT reads fastq file with ONT reads
  • File
lineage lineage lineage for BUSCO, e.g.: arthropoda_odb10, vertebrata_odb10, mammalia_odb10...
  • string
meryl db meryl db import meryldb to run merqury on the assemblies obtained
  • File

Steps

ID Name Description
6 Flatten collection __FLATTEN__
7 Flye toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0
8 Parse parameter value param_value_from_file
9 Parse parameter value param_value_from_file
10 Parse parameter value param_value_from_file
11 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0
12 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0
13 Bandage Image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
14 BUSCO flye toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0
15 Merqury flye toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2
16 gfastats flye toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
17 Merge BAM Files toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0
18 HyPo toolshed.g2.bx.psu.edu/repos/iuc/hypo/hypo/1.0.3+galaxy0
19 Merqury Hypo merqury on flye assembly polished with 1 round of hypo toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2
20 gfastats Hypo toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
21 BUSCO Hypo toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0

Outputs

ID Name Description Type
consensus consensus n/a
  • File
assembly_gfa assembly_gfa n/a
  • File
_anonymous_output_1 _anonymous_output_1 n/a
  • File
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
  • File
_anonymous_output_2 _anonymous_output_2 n/a
  • File
Busco on input dataset(s): short summary Busco on input dataset(s): short summary 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
Merqury on input dataset(s): plots Merqury on input dataset(s): plots n/a
  • File
QV stats QV stats n/a
  • File
Merqury on input dataset(s): stats Merqury on input dataset(s): stats n/a
  • File
_anonymous_output_6 _anonymous_output_6 n/a
  • File
output1 output1 n/a
  • File
HyPo on input dataset(s): polished assembly HyPo on input dataset(s): polished assembly 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

Version History

Version 1 (earliest) Created 11th Mar 2024 at 12:41 by Diego De Panis

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Created: 11th Mar 2024 at 12:41

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