IDBA-hybrid protocols

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description
IDBA-hybrid computational protocol

IDBA-hybrid specifications

Information


Unique identifier OMICS_20111
Name IDBA-hybrid
Alternative name Iterative De Bruijn graph de novo Assembler-hybrid for hybrid sequencing
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 1.1.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Peng Yu <>

IDBA-hybrid IN pipelines

 (2)
2016
PMCID: 5028885
PMID: 27645766
DOI: 10.1038/srep33670

[…] into contigs using idba-ud20, and by comparing them to francisella genome sequences, fle contigs were identified. all trimmed reads were mapped to these contigs and then reassembled with idba-ud and idba-hybrid into a final set of seven contigs (supplementary table s3), which were submitted to ncbi (accession: lvce00000000). the completeness of the assembled genome was examined using […]

2016
PMCID: 5072711
PMID: 27764207
DOI: 10.1371/journal.pone.0165019

[…] two clinical strains and six laboratory-evolved mutants. in addition, an 8-kb mate-pair library was prepared for xh209 to complete its genome [16]. the raw illumina data were de novo assembled using idba-hybrid [17]. the pre-assembled contigs were arranged into scaffolds using sspace [18], and gaps within the scaffolds were closed with gapfiller [19]. mapping and snp detection were performed […]

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