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Bionano Hybrid Scaffold (version 3.7.0+galaxy3)

NGS FASTA:

Input NGS FASTA

BioNano CMAP:

Input BioNano CMAP

Configuration mode:

It defines the parameters used in each step of hybrid scaffold

Restriction enzyme:

Define single enzyme for in-silico FASTA to CMAP digestion. Avalible enzymes: BspQI, BbvCI, BsmI, BsrDI, BssSI, DLE1.

Conflict resolution file:

Input a conflict resolution file indicating which NGS and BioNano conflicting contigs to be cut [optional]

Genome maps conflict filter:

Conflict filter level genome maps [required if not using -M option]

Sequences conflict filter:

Conflict filter level for sequences [required if not using -M option]

Provide BisCot required files:

Generate a collection with the files contained in the hybrid_scaffolds folder

Generate an output package in ZIP format:

The hybrid scaffold output package (.zip) can be imported into Access for visualization

Remove BioNano cut sites:

This option removes the spurious BioNano cut sites that are inserted into gaps in some assemblies, replacing them with Ns.

Purpose

The Hybrid Scaffold pipeline automates the comprehensive scaffolding process and is consisted of five major steps: 1) generate in silico maps for sequence assembly; 2) align in silico sequence maps against Bionano genome maps to identify and resolve potential conflicts in either data set; 3) merge the non-conflicting maps into hybrid scaffolds; 4) align sequence maps to the hybrid scaffolds; and 5) generate AGP and FASTA files for the scaffolds.

Coverage

For Hybrid Scaffold, we recommend using as input a minimum of 80X effective molecule coverage in order to build an accurate and contiguous consensus genome map assembly for each enzyme. When using nickases, using more coverage does not significantly improve map contiguity. When using a DLS enzyme such as DLE-1, effective coverage up to and beyond 100X has shown improved map contiguities for some plants and animals.

Input Bionano assembly

When running the de novo assembly pipeline for hybrid scaffolding applications, users are recommended to use assembly parameters for non-haplotype-aware assembly. The current Hybrid Scaffold pipeline does not explicitly handle haplotype information and assumes there is only one genome map or NGS sequence contig covering a given genomic region. If multiple haplotypes are present, the pipeline may make false positive conflict cuts and incorrectly mix haplotypes in the final scaffolds. We understand that haplotype information is important in many applications, and a fully haplotype-aware Hybrid Scaffold pipeline is in our roadmap for a future release.

Bionano Genomics has agreed to provide the licensed Bionano Solve software to enable the VGP to package the software in a container. Bionanno Solve as shipped in this container may not be the latest and may not run efficiently on non-validated hardware. Hence, it is not supported by Bionano Genomics. Any questions concerning this version should be passed to the VGP (https://github.com/VGP/vgp-assembly/issues) or Galaxy community (https://help.galaxyproject.org). For the latest supported Bionano software, visit Bionano Support https://bionanogenomics.com/support/