GAAP Genome-organization-framework Assisted Assembly Pipeline

Introduction

GAAP is a cGOF (core-gene-defined Genome-organization-framework) Assisted Assembly Pipeline. It is aimed at scaffolding and extending scaffolds and contigs based on de novo assembly of one paired-end library and core gene cluster from multiple related references.

GAAP is composed of two separate yet sequential sections:

1) cGOF_identification, which extracts sequences and order & orientation of cGOF segments from references; one species run once.

2) Scaffolding, which uses segments of cGOF genes as anchors to order the target scaffolds and contigs, uses paired-end reads mapping for local scaffolding of ordered scaffolds/contgis to recover more contigs, and then matches the closest organized reference to construct a pseudogenome; one target run once.

Publications

  1. GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes
    Yuan,Lina, Yu,Yang, Zhu,Yanmin, Li,Yulai, Li,Changqing, Li,Rujiao, Ma,Qin, Siu,Gilman Kit-Hang, Yu,Jun, Jiang,Taijiao, Xiao,Jingfa, Kang,Yu, 2017/1/25 - BMC Genomics

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Summary
AccessionBT000008
Tool TypePipeline & Protocol
CategoryGenome assembly data
PlatformsLinux/Unix
TechnologiesPython2
User InterfaceTerminal Command Line
Input DataFASTA, FASTQ
Latest Release1.0 (June 27, 2017)
Download Count308
Country/RegionChina
Submitted Byxiaojingfa@big.ac.cn