NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly.

ABSTRACT:

Background

Deep shotgun sequencing on next generation sequencing (NGS) platforms has contributed significant amounts of data to enrich our understanding of genomes, transcriptomes, amplified single-cell genomes, and metagenomes. However, deep coverage variations in short-read data sets and high sequencing error rates of modern sequencers present new computational challenges in data interpretation, including mapping and de novo assembly. New lab techniques such as multiple displacement amplification (MDA) of single cells and sequence independent single primer amplification (SISPA) allow for sequencing of organisms that cannot be cultured, but generate highly variable coverage due to amplification biases.

Results

Here we introduce NeatFreq, a software tool that reduces a data

SUBMITTER: McCorrison JM 

PROVIDER: S-EPMC4245761 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature