VGP purge assembly with purge_dups pipeline
Version 1

Workflow Type: Galaxy
Work-in-progress

Purge Phased assembly of duplications and overlaps. Include purge steps for Primary and Alternate assemblies.

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Inputs

ID Name Description Type
Genomescope model parameters n/a n/a
  • File
Hifiasm Alternate assembly n/a From the Hifiasm workflow. In fasta format.
  • File
Hifiasm Primary assembly n/a From the Hifiasm workflow. In fasta format.
  • File
Pacbio Reads Collection - Trimmed n/a Collection of trimmed reads (from cutadapt in the Hifiasm workflow) in fastq format.
  • File

Steps

ID Name Description
10_Cut n/a n/a
11_Parse parameter value n/a n/a
12_Parse parameter value n/a n/a
13_Purge overlaps n/a n/a
14_Purge overlaps n/a n/a
15_Purge overlaps n/a n/a
16_Concatenate datasets n/a n/a
17_Map with minimap2 n/a n/a
18_Purge overlaps n/a n/a
19_Purge overlaps n/a n/a
20_Map with minimap2 n/a n/a
21_Purge overlaps n/a n/a
22_Purge overlaps n/a n/a
4_Map with minimap2 n/a n/a
5_Purge overlaps n/a n/a
6_Compute n/a n/a
7_Map with minimap2 n/a n/a
8_Compute n/a n/a
9_Cut n/a n/a

Version History

Version 1 (earliest) Created 5th Apr 2022 at 23:16 by Cristóbal Gallardo

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Created: 5th Apr 2022 at 23:16

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