Assembly-Hifi-HiC-phasing-VGP4
- Author(s):
- Galaxy
- VGP
- Delphine Lariviere
- Release: 0.2.2
- License: CC-BY-4.0
- UniqueID: cb0e2983-13df-451c-85a2-ee78c94a2bd2
Contiging Solo w/HiC:
Generate phased assembly based on PacBio Hifi Reads using HiC data from the same individual for phasing.
Inputs
- Hifi long reads [fastq]
- HiC forward reads (if multiple input files, concatenated in same order as reverse reads) [fastq]
- HiC reverse reads (if multiple input files, concatenated in same order as forward reads) [fastq]
- K-mer database [meryldb]
- Genome profile summary generated by Genomescope [txt]
- Name of first assembly
- Name of second assembly
Outputs
- Haplotype 1 assembly ([fasta] and [gfa])
- Haplotype 2 assembly ([fasta] and [gfa])
- QC: BUSCO report for both assemblies
- QC: Merqury report for both assemblies
- QC: Assembly statistics for both assemblies
- QC: Nx plot for both assemblies
- QC: Size plot for both assemblies
Changelog
[0.2.2] 2024-08-07
- Expose parameter: Busco lineage database
[0.2.1] 2024-07-29
Automatic update
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy1
was updated totoolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1
toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1
was updated totoolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0
[0.2] 2024-07-12
Added
- Workflow report
Changed
- Fix bug where the columns of the assembly statistics didn't join properly.
[0.1.11] 2024-05-20
Automatic update
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy0
was updated totoolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy1
[0.1.10] 2024-04-23
Changed
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.7+galaxy0
was updated totoolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy0
[0.1.9] 2024-04-19
Manual Updates
- Add the option to provide Homozygous Read coverage parameter
Automatic update
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0
was updated totoolshed.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 totoolshed.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 totoolshed.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 totoolshed.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 totoolshed.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 totoolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4
[0.1.8] 2024-03-25
Manual update
- Remove tag filtering
- Add merqury histogram output
- Add output for cutadapt
- Output Gff files in Busco
Automatic update
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
was updated totoolshed.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 totoolshed.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 totoolshed.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 totoolshed.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 totoolshed.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 totoolshed.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 totoolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1
[0.1.7] 2023-11-20
- Fix author in dockstore
[0.1.5] 2023-11-15
Added
- more descriptive labels for inputs
Automatic update
toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0
was updated totoolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0
[0.1.4] 2023-11-08
Automatic update
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1
was updated totoolshed.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 totoolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2
was updated totoolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0
was updated totoolshed.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 totoolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3
toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0
was updated totoolshed.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 totoolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1
[0.1.3] - 2023-11-08
- Added tags
hifiasm_Assembly_Haplotype_1
andhifiasm_Assembly_Haplotype_2
to fasta outputs of hifiasm, so they can be easily identified for feeding to purge_dups workflow - Made BUSCO lineages selectable from workflow launch interface
[0.1.2] - 2023-11-07
- Added input filtering based on tags. Rearranged input ordering.
[0.1] - 2023-09-27
- Creation of workflow for HiFi assembly with Hi-C phasing.
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/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/iuc/pick_value/pick_value/0.2.0
- 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/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
- toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1
- join1
- 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_cut_tool/9.3+galaxy1
- __EXTRACT_DATASET__
- toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1