Genome Assembly using PacBio data
1.0

Workflow Type: Galaxy

Genome Assembly using PacBio data and Flye or Hifiasm assembler

Associated Tutorial

This workflows is part of the tutorial Genome assembly using PacBio data, available in the GTN

Features

Thanks to...

Workflow Author(s): Erwan Corre, Stéphanie Robin, Anthony Bretaudeau, Alexandre Cormier, Solenne Correard

Tutorial Author(s): Anthony Bretaudeau, Alexandre Cormier, Erwan Corre, Laura Leroi, Stéphanie Robin, Solenne Correard

Tutorial Contributor(s): Helena Rasche, Anthony Bretaudeau, Stéphanie Robin, Cristóbal Gallardo, Saskia Hiltemann, Björn Grüning, Solenne Correard, Bérénice Batut

Grants(s): Gallantries: Bridging Training Communities in Life Science, Environment and Health

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
PacBio reads #main/PacBio reads PacBio reads in fastq format
  • File
Reference genome #main/Reference genome Reference genome from JGI
  • File

Steps

ID Name Description
2 Flye toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9+galaxy0
3 Fasta Statistics toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0
4 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2
5 Fasta Statistics toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0
6 Quast toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy3
7 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2

Outputs

ID Name Description Type
Flye on input dataset(s): assembly graph #main/Flye on input dataset(s): assembly graph n/a
  • File
Flye on input dataset(s): assembly info #main/Flye on input dataset(s): assembly info n/a
  • File
Flye on input dataset(s): consensus #main/Flye on input dataset(s): consensus n/a
  • File
Flye on input dataset(s): graphical fragment assembly #main/Flye on input dataset(s): graphical fragment assembly n/a
  • File
Quast on input dataset(s): HTML report #main/Quast on input dataset(s): HTML report n/a
  • File
_anonymous_output_1 #main/_anonymous_output_1 n/a
  • File
_anonymous_output_2 #main/_anonymous_output_2 n/a
  • File

Version History

1.0 (earliest) Created 2nd Jun 2025 at 11:01 by GTN Bot

Added/updated 4 files


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Created: 2nd Jun 2025 at 11:01

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