Contiging Solo:

Generate assembly based on PacBio Hifi Reads.

Inputs

1. Hifi long reads [fastq]
2. K-mer database [meryldb]
3. Genome profile summary generated by Genomescope [txt]
4. Homozygous Read Coverage. Optional, use if you think the estimation from Genomescope is inacurate.
5. Genomescope Model Parameters generated by Genomescope [tabular]
6. Database for busco lineage (recommended: latest)
7. Busco lineage (recommended: vertebrata)
8. Name of first assembly
9. Name of second assembly

Outputs

1. Primary assembly
2. Alternate assembly
3. QC: Bandage image for the raw unitigs
4. QC: BUSCO report for both assemblies
5. QC: Merqury report for both assemblies
6. QC: Assembly statistics for both assemblies
7. QC: Nx plot for both assemblies
8. QC: Size plot for both assemblie

Changelog

[0.2.1] 2024-08-13

• Expose Busco lineage database parameter

[0.2] 2024-08-01

Added

• Add bandage image
• Add workflow report

Changed

• Fix bug in merging assembly statistics

[0.1.8] 2024-07-22

Automatic update

• toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1

[0.1.7] 2024-07-15

Automatic update

• toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy1 was updated to toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0

[0.1.6] 2024-05-20

Automatic update

• toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy1
• toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.1.0 was updated to toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0

[0.1.5] 2024-04-23

Changed

• toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.7+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy0

[0.1.4] 2024-04-19

Manual Updates

• Add Homozygous Read coverage parameter and calculation
• Expose Lineage parameter

Automatic update

• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1
• 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_cat/9.3+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1
• toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3 was updated to toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4

[0.1.3] 2024-03-25

Manual Updates

• Add Gff outputs to Busco
• Add histogram outputs to Merqury
• Add labels to subworkflows

Automatic update

• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy0
• 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_sed_tool/1.1.1 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy0
• toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.7+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1

[0.1.2] 2023-11-14

Automatic update

• toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1 was updated to toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.16.1+galaxy4 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy0
• 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/merqury/merqury/1.3+galaxy2 was updated to toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3
• 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/devteam/add_value/addValue/1.0.0 was updated to toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1
• 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] 2023-11-20

• Fix author in dockstore

[0.1] - 2023-09-26

Addition of the workflow to the iwc repository.

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/lparsons/cutadapt/cutadapt/4.9+galaxy1
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1
• toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
• toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0
• toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1
• Cut1
• Convert characters1
• param_value_from_file
• toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0
• toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4
• toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
• toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0
• toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
• __EXTRACT_DATASET__
• join1
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1