Workflow Type: Galaxy
Stable

Purge-duplicates-from-hifiasm-assembly

General recommendations for using Purge-duplicates-from-hifiasm-assembly

Please see the Genome assembly with hifiasm on Galaxy Australia guide.

Acknowledgements

The workflow & the doc_guidelines template used are supported by the Australian BioCommons via Bioplatforms Australia funding, the Australian Research Data Commons (https://doi.org/10.47486/PL105) and the Queensland Government RICF programme. Bioplatforms Australia and the Australian Research Data Commons are enabled by the National Collaborative Research Infrastructure Strategy (NCRIS).

Inputs

ID Name Description Type
HiFi reads as FASTQ HiFi reads as FASTQ n/a
  • File
HiFiASM 1o assembly HiFiASM 1o assembly n/a
  • File

Steps

ID Name Description
2 Step 1. Base-level coverage toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy3
3 Step 1. Run minimap2 to align pacbio data and generate paf files, toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.20+galaxy2
4 Step 1. Split an assembly and do a self-self alignment toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.20+galaxy2
5 Step 1. then calculate read depth histogram and base-level read depth. toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy3
6 Step 2. Purge haplotigs and overlaps toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy3
7 Step 3. Get purged primary and haplotig sequences from draft assembly toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy3
8 Haplotype fasta toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.3

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
Purge overlaps on input dataset(s): purge_dups log file Purge overlaps on input dataset(s): purge_dups log file n/a
  • File
Purge overlaps on input dataset(s): purge_dups bed file Purge overlaps on input dataset(s): purge_dups bed file 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

Version History

v1.0.0 (latest) Created 17th Oct 2022 at 03:53 by Johan Gustafsson

Add workflow + update documentation


Frozen v1.0.0 8ecf989

Version 1 (earliest) Created 15th Nov 2021 at 01:39 by Johan Gustafsson

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Frozen Version-1 d37b742
help Creators and Submitter
Creator
Additional credit

Gareth Price

Submitter
Citation
Price, G. (2022). Purge duplicates from hifiasm assembly v1.0. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.237.2
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Created: 15th Nov 2021 at 01:39

Last updated: 17th Oct 2022 at 03:53

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