VGP HiFi phased assembly with hifiasm and HiC data
Version 1

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Workflow Type: Galaxy
Work-in-progress

Performs Long Read assembly using PacBio data and Hifiasm. Part of VGP assembly pipeline. This workflow generate a phased assembly.

SEEK ID: https://workflowhub.eu/workflows/318?version=1

Inputs

ID Name Description Type
HiC forward reads n/a n/a
  • File
HiC reverse reads n/a n/a
  • File
Meryl Database n/a Database Generated from the "Meryl database creation" workflow.
  • File
Pacbio Reads Collection n/a Collection of Long reads in fastq format.
  • File

Steps

ID Name Description
10_Hifiasm n/a n/a
11_Search in textfiles n/a n/a
12_GFA to FASTA n/a n/a
13_GFA to FASTA n/a n/a
14_gfastats n/a n/a
15_gfastats n/a n/a
16_Replace Text n/a n/a
17_Busco n/a n/a
18_Merqury n/a n/a
19_Busco n/a n/a
20_Convert n/a n/a
21_Cut n/a n/a
22_Parse parameter value n/a n/a
23_Quast n/a n/a
24_Quast n/a n/a
25_gfastats n/a n/a
26_gfastats n/a n/a
2_Input parameter n/a n/a
3_Input parameter n/a n/a
4_Input parameter n/a n/a
7_Meryl n/a n/a
8_Cutadapt n/a n/a
9_GenomeScope n/a n/a

Version History

Version 1 (earliest) Created 5th Apr 2022 at 22:55 by Cristóbal Gallardo

Initial commit


Open master abcf2a9
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Submitter
License
GNU General Public License v3.0 only (GPL-3.0)
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Views: 6021   Downloads: 545   Runs: 4

Created: 5th Apr 2022 at 22:55

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Total size: 61.7 KB
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