VGP hybrid scaffolding with HiC data
Version 1

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Workflow Type: Galaxy

Work-in-progress

Performs scaffolding using HiC Data. Part of VGP assembly pipeline. The scaffolding can be performed on long read assembly contigs or on scaffolds (e.g.: Bionano scaffolds).

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SEEK ID: https://workflowhub.eu/workflows/324?version=1

Inputs

ID	Name	Description	Type
Estimated genome size - Parameter File	n/a	Parameter file generated in the VGP Hifiasm workflow. Estimated reference genome size (in bp) for computing NGx statistics	File
HiC Forward reads	n/a	HiC forward reads in Fastq Format. The reads must be in the same order as reverse reads.	File
HiC reverse reads	n/a	HiC reverse reads in Fastq Format. The reads must be in the same order as forward reads.	File
Restriction enzyme sequences	n/a	File containing the list of restriction enzymes used by Arima technology, the sequences are separated by a comma. In the VGP project AWS, the restriction enzyme sequences can be found in the repository containing HiC data.	File
Scaffolded Assembly	n/a	Scaffold generated by "VGP Bionano" workflows or contigs Generated by the "VGP Hifiasm" workflow.	File
Sequence graph - Optional	n/a	Sequence graphs encoded in GFA format. (-g)	File

Steps

ID	Name	Description
10_Parse parameter value	n/a	n/a
11_Parse parameter value	n/a	n/a
12_Filter and merge	n/a	n/a
13_bedtools BAM to BED	n/a	n/a
14_PretextMap	n/a	n/a
15_Sort	n/a	n/a
16_Pretext Snapshot	n/a	n/a
17_SALSA	n/a	n/a
18_Busco	n/a	n/a
19_BWA-MEM2	n/a	n/a
20_BWA-MEM2	n/a	n/a
21_Quast	n/a	n/a
22_Filter and merge	n/a	n/a
23_PretextMap	n/a	n/a
24_Pretext Snapshot	n/a	n/a
6_Input parameter	n/a	n/a
7_Replace	n/a	n/a
8_BWA-MEM2	n/a	n/a
9_BWA-MEM2	n/a	n/a