TreeToReads - a pipeline for simulating raw reads from phylogenies.

ABSTRACT:

Background

Using phylogenomic analysis tools for tracking pathogens has become standard practice in academia, public health agencies, and large industries. Using the same raw read genomic data as input, there are several different approaches being used to infer phylogenetic tree. These include many different SNP pipelines, wgMLST approaches, k-mer algorithms, whole genome alignment and others; each of these has advantages and disadvantages, some have been extensively validated, some are faster, some have higher resolution. A few of these analysis approaches are well-integrated into the regulatory process of US Federal agencies (e.g. the FDA's SNP pipeline for tracking foodborne pathogens). However, despite extensive validation on benchmark datasets and comparison with other pipelin

SUBMITTER: McTavish EJ 

PROVIDER: S-EPMC5359950 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature