hi-c-contact-map-for-assembly-manual-curation/main
v1.0beta2 (latest)

v1.0beta2 (latest)

v1.0beta1 (earliest)

Workflow Type: Galaxy

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=2

Steps

ID	Name	Description
10	Hap2 not provided	toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
11	Add suffix to 2 haplotypes	n/a
12	concatenate HiFi	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy0
13	Add Suffix 1 haplotype	n/a
14	Pick Assembly	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
15	Trim and Align Hi-C paired collection	n/a
16	gfastats	toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0
17	seqtk_telo	toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_telo/1.4+galaxy0
18	Map with minimap2	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1
19	PretextMap	toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1
20	Compute	toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
21	Cut	Cut1
22	bamCoverage	toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.4+galaxy0
23	Compute	toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
24	Add Coverage Track	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0
25	Test if telomere track is empty	param_value_from_file
26	False if telomere track is empty	toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
27	Add telomere track	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0
28	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
29	Add gaps track	toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0
30	Pretext Snapshot	toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0
31	Extract dataset	__EXTRACT_DATASET__