NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language.

ABSTRACT:

Background

Shotgun metagenomes contain a sample of all the genomic material in an environment, allowing for the characterization of a microbial community. In order to understand these communities, bioinformatics methods are crucial. A common first step in processing metagenomes is to compute abundance estimates of different taxonomic or functional groups from the raw sequencing data. Given the breadth of the field, computational solutions need to be flexible and extensible, enabling the combination of different tools into a larger pipeline.

Results

We present NGLess and NG-meta-profiler. NGLess is a domain specific language for describing next-generation sequence processing pipelines. It was developed with the goal of enabling user-friendly computational reproducibility. It

SUBMITTER: Coelho LP 

PROVIDER: S-EPMC6547473 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature