hi-c-contact-map-for-assembly-manual-curation/main
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Workflow Type: Galaxy

Tests Not available

This workflow generates Hi-C contact maps for genome assemblies in the Pretext format. It is compatible with one or 2 haplotypes. It includes tracks for PacBio read coverage, Gaps, and telomeres. The Pretext files can be open in PretextView for the manual curation of genome assemblies.

SEEK ID: https://workflowhub.eu/workflows/1327?version=8

Steps

ID	Name	Description
19	Compose text parameter value	toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
20	Hap2 not provided	toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
21	Add suffix to 2 haplotypes	n/a
22	Map parameter value	toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
23	Test if collection has only one item or is empty	n/a
24	Cutadapt	toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.2+galaxy1
25	Add Suffix 1 haplotype	n/a
26	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
27	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
28	Pick Assembly	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
29	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
30	compleasm	toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy3
31	Trim and Align Hi-C paired collection	n/a
32	Teloscope	toolshed.g2.bx.psu.edu/repos/iuc/teloscope/teloscope/0.1.3+galaxy1
33	gfastats	toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1
34	Map with minimap2	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2
35	compleasm	toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy3
36	Hybrid dedup	n/a
37	Duplication Stats	n/a
38	Select Q telomeres	Filter1
39	Select P telomeres	Filter1
40	Compute	toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
41	Samtools merge	toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.22+galaxy1
42	Extract dataset	__EXTRACT_DATASET__
43	Concatenate datasets	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3
44	Pick Alignements	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
45	Pick Hi-C duplication stats	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
46	Pick Hi-C duplication report	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
47	Q telomere bed	Cut1
48	P telomere bed	Cut1
49	Hifi Alignments	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
50	GFF-to-BED	gff2bed1
51	PretextMap	toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.3+galaxy0
52	PretextMap - Multimapping	toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.3+galaxy0
53	Test if Q telomere track is empty	param_value_from_file
54	Test if P telomere track is empty	param_value_from_file
55	bamCoverage	toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.4+galaxy0
56	Samtools depth	toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.22+galaxy1
57	Keep CDS	Filter1
58	False if Q telomere track is empty	toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
59	False if P telomere track is empty	toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
60	Add Coverage Track - Multimapping	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
61	Add Coverage Track	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
62	Filter	Filter1
63	Unique lines	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.5+galaxy3
64	Add P telomere track - Multimapping	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
65	Add P telomere track	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
66	Compute	toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
67	Cut	Cut1
68	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
69	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
70	Cut	Cut1
71	Add column	toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1
72	Add Q telomere track - Multimapping	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
73	Add Q telomere track	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
74	bedtools MergeBED	toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1+galaxy2
75	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
76	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
77	Add column	toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1
78	Add gaps track - Multimapping	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
79	Add gaps track	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
80	Add coverage gaps track - Multimapping	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
81	Add genes track	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
82	Add gene track - Multimapping	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
83	Add coverage gaps track	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.9+galaxy0
84	Pretext Snapshot	toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.5+galaxy1
85	Pretext Snapshot	toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.5+galaxy1
86	Extract dataset	__EXTRACT_DATASET__
87	Extract dataset	__EXTRACT_DATASET__