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Synteny-based chromosome scaffolding (Pieridae)

Subcategory: genome assembly
Papers: 1 | Mentions: 1

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Knowledge graph centered on Synteny-based chromosome scaffolding (Pieridae) with 31 nodes and 109 connections. Top connected: Ligusticum porteri, Lepidoptera, Papilio, non-native plants, Pieris napi.

Description

Using synteny analysis with a closely related reference genome to arrange contigs into chromosome-level scaffolds using MUMmer alignment and RagTag scaffolding.

Typical Equipment

  • nucmer (MUMmer4, v.4.0.0beta2)
  • RagTag

Output Measurements

  • pseudo-chromosomal assembly
  • synteny blocks
  • chromosome assignments

Papers Using This Protocol (1)

article

The genome of the Margined White butterfly (Pieris macdunnoughii): sex chromosome insights and the power of polishing with PoolSeq data

2021Genome Biology and Evolutionusing

Species Studied With This Protocol

Lepidoptera

1 paper

native fish

1 paper

non-native plants

1 paper

Arthropoda

1 paper

native fish species

1 paper

Ligusticum porteri

Apiaceae1 paper

native fishes

1 paper

Pieris napi

Pieridae1 paper

Pieris macdunnoughii

Pieridae1 paper

Alliaria petiolata

Brassicaceae1 paper