Scaffolding with HiC data

This workflow perfoms scaffolding using HiC data with YAHS. It is designed to be run as part of one the VGP analysis trajectories. Example of trajectory :

• VGP1 : Kmer profiling
• VGP4 : Genome assembly with HiC phasing
• VGP6 : Purge duplicated haplotigs
• VGP8 : Scaffolding with HiC

Inputs

1. Scaffolded assembly [fasta]
2. Database for busco lineage (recommended: latest)
3. Busco lineage (recommended: vertebrata)
4. Concatenated HiC forward reads [fastq]
5. Concatenated HiC reverse reads [fastq]
6. Restriction enzyme sequence (recommended for VGP data: Arima Hi-C 2.0)
7. Estimated genome size [txt]
8. Haplotype name

Outputs

1. Scaffolds in [fasta] and [gfa] format
2. QC: Assembly statistics
3. QC: Nx plot
4. QC: Size plot
5. QC: BUSCO report
6. QC: Pretext Maps before and after scaffolding

Changelog

[0.2.8] 2024-09-12

• Add suffix to the scaffold names corresponding to the haplotype being assembled

[0.2.7] 2024-08-13

• Expose Busco lineage database parameter

[0.2.6] 2024-08-05

Automatic update

• toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy1 was updated to toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy2

[0.2.5] 2024-07-31

• Addition of Workflow report

[0.2.4] 2024-05-20

Automatic update

• toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2 was updated to toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0

[0.2.3] 2024-04-01

Automatic update

• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1

[0.2.2] 2024-02-05

Manual update

• remove tag filtering
• set "Show grid" of Pretext Snapshot to "yes"

Automatic update

• toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1
• toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1 was updated to toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0

[0.2.1] 2023-11-20

• Fix author in dockstore

[0.2] - 2023-11-15

Added

• more descriptive labels for inputs

[0.1.2] 2023-11-14

Automatic update

• toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
• toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1
• toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy1
• toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0
• toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2 was updated to toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0
• toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1

[0.1.1] - 2023-10-26

Added tags for better visibility of outputs in the history, and exposure of the BUSCO lineage parameter

[0.1] - 2023-09-27

Creation of the workflow and tests

The following tools are required to run this workflow.

This will eventually be a pretty page with links to each tool in the (new) toolshed, etc.

• toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
• param_value_from_file
• toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
• toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1
• toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1
• toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1
• toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy2
• toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1
• __EXTRACT_DATASET__
• toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0
• Cut1
• toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0
• toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1