InteMAP: Integrated metagenomic assembly pipeline for NGS short reads.

ABSTRACT:

Background

Next-generation sequencing (NGS) has greatly facilitated metagenomic analysis but also raised new challenges for metagenomic DNA sequence assembly, owing to its high-throughput nature and extremely short reads generated by sequencers such as Illumina. To date, how to generate a high-quality draft assembly for metagenomic sequencing projects has not been fully addressed.

Results

We conducted a comprehensive assessment on state-of-the-art de novo assemblers and revealed that the performance of each assembler depends critically on the sequencing depth. To address this problem, we developed a pipeline named InteMAP to integrate three assemblers, ABySS, IDBA-UD and CABOG, which were found to complement each other in assembling metagenomic sequences. Making a decision o

SUBMITTER: Lai B 

PROVIDER: S-EPMC4545859 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature