Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation.

ABSTRACT:

Background

Microbiome-wide gene expression profiling through high-throughput RNA sequencing ('metatranscriptomics') offers a powerful means to functionally interrogate complex microbial communities. Key to successful exploitation of these datasets is the ability to confidently match relatively short sequence reads to known bacterial transcripts. In the absence of reference genomes, such annotation efforts may be enhanced by assembling reads into longer contiguous sequences ('contigs'), prior to database search strategies. Since reads from homologous transcripts may derive from several species, represented at different abundance levels, it is not clear how well current assembly pipelines perform for metatranscriptomic datasets. Here we evaluate the performance of four currently empl

SUBMITTER: Celaj A 

PROVIDER: S-EPMC4236897 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature