De Novo Genome Assembly with Long Reads

The user needs to create a draft assembly using a de novo assembly method of choice (e.g. Velvet [1 (link)], SOAPdenovo [2 (link)], Ray [18 (link)], CLCbio (CLC bio, Aarhus, Denmark) or Newbler (Roche)). Optionally the user may also provide scaffold sequences generated with dedicated software (e.g. SSPACE [5 (link)] or SOPRA [4 (link)]). The resulting contigs or scaffolds (in FASTA format) are to be provided as input to SSPACE-LongRead software together with a set of long reads in FASTQ or FASTA format (e.g. PacBio CLR reads). Note that in our study we observe that SSPACE-LongRead obtains the best results if the draft assembly is constructed with CLCbio or Newbler as these tend to better split contigs at repeat boundaries (see the Results and Discussion section for additional explanations).

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Boetzer M, & Pirovano W. (2014). SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information. BMC Bioinformatics, 15, 211.

Publication 2014

CLCbio Newbler

Corresponding Organization :

Other organizations : Bioclear Earth (Netherlands)

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Protocol cited in 28 other protocols

Variable analysis

independent variables

De novo assembly method of choice (e.g. Velvet, SOAPdenovo, Ray, CLCbio, Newbler)
Scaffold sequences generated with dedicated software (e.g. SSPACE, SOPRA)

dependent variables

Resulting contigs or scaffolds (in FASTA format)

control variables

Long reads in FASTQ or FASTA format (e.g. PacBio CLR reads)

notes

The authors note that SSPACE-LongRead obtains the best results if the draft assembly is constructed with CLCbio or Newbler, as these tend to better split contigs at repeat boundaries.

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