QUAST: quality assessment tool for genome assemblies

 At 2013-09-26 12:30:44 AM  |   96

Here, we present QUAST-a quality assessment tool for evaluating and comparing genome assemblies. This tool improves on leading assembly comparison software with new ideas and quality metrics. Read more

IDBA-UD: A single cell assembler.

 At 2013-09-26 12:30:58 AM  |   285

IDBA-UD: an algorithm that is based on the de Bruijn graph approach for assembling reads from single-cell sequencing or metagenomic sequencing technologies with uneven sequencing depths.  Read more

C-Sibelia: an easy-to-use and highly accurate tool for bacterial genome comparison

 At 2013-11-25 09:58:11 AM  |   423

We present Comparative Sibelia software (C-Sibelia) for the comparison of two bacterial genomes in the form of complete sequences or draft assemblies. C-Sibelia is able to compare genomes in the presence of rearrangements and duplications. C-Sibelia takes as input two FASTA files (the assembly and reference files; if the reference genome is not available, it can be substituted by another draft assembly) and produces: (1) a VCF file containing all identified single nucleotide variations (SNVs) and indels; (2) annotation of these variants by SnpEff; (3) an XMFA1 file containing alignment information. The web-based version also produces a circular diagram visualizing the rearrangement of synteny blocks in two genomes. Read more

De novo genome assembly: what every biologist should know

 At 2014-02-27 07:24:38 AM  |   304

Asked how mature the field of genome assembly is, Ian Korf at the University of California, Davis, compares it to a teenager with great capabilities. “It's got bold assertions about what it can do, but at the same time it's making embarrassing mistakes,” he says. Perhaps the biggest barrier to maturity is that there are few ways to distinguish true insight from foolish gaffe. When a species' genome is newly assembled, no one knows what's real, what's missing, and what's experimental artifact. Read more

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

 At 2013-09-26 12:31:09 AM  |   421

Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly. Read more

From Indexing Data Structures to de Bruijn Graphs

 At 2014-10-31 03:03:42 PM  |   287

New technologies have tremendously increased sequencing throughput compared to traditional techniques, thereby complicating DNA assembly. Read more