VGP hybrid scaffolding with HiC data
Version 1

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).

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

Version History

Version 1 (earliest) Created 5th Apr 2022 at 00:33 by Cristóbal Gallardo

Initial commit


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Created: 5th Apr 2022 at 00:33

Last used: 28th Jun 2022 at 16:09

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