Workflow Type: Galaxy
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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).
Could not render the workflow diagram.
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 |
|
HiC Forward reads | n/a | HiC forward reads in Fastq Format. The reads must be in the same order as reverse reads. |
|
HiC reverse reads | n/a | HiC reverse reads in Fastq Format. The reads must be in the same order as forward reads. |
|
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. |
|
Scaffolded Assembly | n/a | Scaffold generated by "VGP Bionano" workflows or contigs Generated by the "VGP Hifiasm" workflow. |
|
Sequence graph - Optional | n/a | Sequence graphs encoded in GFA format. (-g) |
|
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
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Created: 5th Apr 2022 at 00:33
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