Assessment of de novo assemblers for draft genomes: a case study with fungal genomes.

ABSTRACT:

Background

Recently, large bio-projects dealing with the release of different genomes have transpired. Most of these projects use next-generation sequencing platforms. As a consequence, many de novo assembly tools have evolved to assemble the reads generated by these platforms. Each tool has its own inherent advantages and disadvantages, which make the selection of an appropriate tool a challenging task.

Results

We have evaluated the performance of frequently used de novo assemblers namely ABySS, IDBA-UD, Minia, SOAP, SPAdes, Sparse, and Velvet. These assemblers are assessed based on their output quality during the assembly process conducted over fungal data. We compared the performance of these assemblers by considering both computational as well as quality metrics. By anal

SUBMITTER: Abbas MM 

PROVIDER: S-EPMC4290589 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature